diff --git a/Cargo.lock b/Cargo.lock
index 3549f0e422..f1209b32ac 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1196,7 +1196,6 @@ dependencies = [
  "dprint-plugin-markdown",
  "dprint-plugin-typescript",
  "env_logger",
- "eszip",
  "fancy-regex",
  "faster-hex",
  "flate2",
@@ -2895,29 +2894,6 @@ version = "1.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "31ae425815400e5ed474178a7a22e275a9687086a12ca63ec793ff292d8fdae8"
 
-[[package]]
-name = "eszip"
-version = "0.79.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8eb55c89bdde75a3826a79d49c9d847623ae7fbdb2695b542982982da990d33e"
-dependencies = [
- "anyhow",
- "async-trait",
- "base64 0.21.7",
- "deno_ast",
- "deno_graph",
- "deno_npm",
- "deno_semver",
- "futures",
- "hashlink 0.8.4",
- "indexmap",
- "serde",
- "serde_json",
- "sha2",
- "thiserror",
- "url",
-]
-
 [[package]]
 name = "fallible-iterator"
 version = "0.3.0"
@@ -3529,15 +3505,6 @@ dependencies = [
  "allocator-api2",
 ]
 
-[[package]]
-name = "hashlink"
-version = "0.8.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e8094feaf31ff591f651a2664fb9cfd92bba7a60ce3197265e9482ebe753c8f7"
-dependencies = [
- "hashbrown",
-]
-
 [[package]]
 name = "hashlink"
 version = "0.9.1"
@@ -5815,7 +5782,7 @@ dependencies = [
  "bitflags 2.6.0",
  "fallible-iterator",
  "fallible-streaming-iterator",
- "hashlink 0.9.1",
+ "hashlink",
  "libsqlite3-sys",
  "smallvec",
 ]
diff --git a/cli/Cargo.toml b/cli/Cargo.toml
index ded6551cd7..14eda5427e 100644
--- a/cli/Cargo.toml
+++ b/cli/Cargo.toml
@@ -84,7 +84,6 @@ deno_runtime = { workspace = true, features = ["include_js_files_for_snapshottin
 deno_semver.workspace = true
 deno_task_shell = "=0.18.1"
 deno_terminal.workspace = true
-eszip = "=0.79.1"
 libsui = "0.4.0"
 node_resolver.workspace = true
 
diff --git a/cli/emit.rs b/cli/emit.rs
index b3f4a4477a..ad200af050 100644
--- a/cli/emit.rs
+++ b/cli/emit.rs
@@ -60,6 +60,7 @@ impl Emitter {
         continue;
       };
 
+      // todo(https://github.com/denoland/deno_media_type/pull/12): use is_emittable()
       let is_emittable = matches!(
         module.media_type,
         MediaType::TypeScript
diff --git a/cli/factory.rs b/cli/factory.rs
index 25f3551102..d5ef4fd8b3 100644
--- a/cli/factory.rs
+++ b/cli/factory.rs
@@ -762,6 +762,7 @@ impl CliFactory {
     let cli_options = self.cli_options()?;
     Ok(DenoCompileBinaryWriter::new(
       self.deno_dir()?,
+      self.emitter()?,
       self.file_fetcher()?,
       self.http_client_provider(),
       self.npm_resolver().await?.as_ref(),
diff --git a/cli/mainrt.rs b/cli/mainrt.rs
index 02d58fcee1..f5b798f817 100644
--- a/cli/mainrt.rs
+++ b/cli/mainrt.rs
@@ -88,11 +88,10 @@ fn main() {
   let standalone = standalone::extract_standalone(Cow::Owned(args));
   let future = async move {
     match standalone {
-      Ok(Some(future)) => {
-        let (metadata, eszip) = future.await?;
-        util::logger::init(metadata.log_level);
-        load_env_vars(&metadata.env_vars_from_env_file);
-        let exit_code = standalone::run(eszip, metadata).await?;
+      Ok(Some(data)) => {
+        util::logger::init(data.metadata.log_level);
+        load_env_vars(&data.metadata.env_vars_from_env_file);
+        let exit_code = standalone::run(data).await?;
         std::process::exit(exit_code);
       }
       Ok(None) => Ok(()),
diff --git a/cli/standalone/binary.rs b/cli/standalone/binary.rs
index 52ee4eeb28..0f8b0b49d4 100644
--- a/cli/standalone/binary.rs
+++ b/cli/standalone/binary.rs
@@ -9,14 +9,18 @@ use std::ffi::OsString;
 use std::fs;
 use std::fs::File;
 use std::future::Future;
+use std::io::ErrorKind;
 use std::io::Read;
 use std::io::Seek;
 use std::io::SeekFrom;
 use std::io::Write;
+use std::ops::Range;
 use std::path::Path;
 use std::path::PathBuf;
 use std::process::Command;
+use std::sync::Arc;
 
+use deno_ast::MediaType;
 use deno_ast::ModuleSpecifier;
 use deno_config::workspace::PackageJsonDepResolution;
 use deno_config::workspace::ResolverWorkspaceJsrPackage;
@@ -30,13 +34,22 @@ use deno_core::futures::AsyncReadExt;
 use deno_core::futures::AsyncSeekExt;
 use deno_core::serde_json;
 use deno_core::url::Url;
+use deno_graph::source::RealFileSystem;
+use deno_graph::ModuleGraph;
+use deno_npm::resolution::SerializedNpmResolutionSnapshot;
+use deno_npm::resolution::SerializedNpmResolutionSnapshotPackage;
+use deno_npm::resolution::ValidSerializedNpmResolutionSnapshot;
+use deno_npm::NpmPackageId;
 use deno_npm::NpmSystemInfo;
+use deno_runtime::deno_fs;
+use deno_runtime::deno_fs::FileSystem;
+use deno_runtime::deno_fs::RealFs;
+use deno_runtime::deno_io::fs::FsError;
 use deno_runtime::deno_node::PackageJson;
 use deno_semver::npm::NpmVersionReqParseError;
 use deno_semver::package::PackageReq;
 use deno_semver::Version;
 use deno_semver::VersionReqSpecifierParseError;
-use eszip::EszipRelativeFileBaseUrl;
 use indexmap::IndexMap;
 use log::Level;
 use serde::Deserialize;
@@ -49,6 +62,7 @@ use crate::args::NpmInstallDepsProvider;
 use crate::args::PermissionFlags;
 use crate::args::UnstableConfig;
 use crate::cache::DenoDir;
+use crate::emit::Emitter;
 use crate::file_fetcher::FileFetcher;
 use crate::http_util::HttpClientProvider;
 use crate::npm::CliNpmResolver;
@@ -60,12 +74,63 @@ use crate::util::fs::canonicalize_path_maybe_not_exists;
 use crate::util::progress_bar::ProgressBar;
 use crate::util::progress_bar::ProgressBarStyle;
 
+use super::file_system::DenoCompileFileSystem;
+use super::serialization::deserialize_binary_data_section;
+use super::serialization::serialize_binary_data_section;
+use super::serialization::DenoCompileModuleData;
+use super::serialization::DeserializedDataSection;
+use super::serialization::RemoteModulesStore;
+use super::serialization::RemoteModulesStoreBuilder;
 use super::virtual_fs::FileBackedVfs;
 use super::virtual_fs::VfsBuilder;
 use super::virtual_fs::VfsRoot;
 use super::virtual_fs::VirtualDirectory;
 
-const MAGIC_TRAILER: &[u8; 8] = b"d3n0l4nd";
+/// A URL that can be designated as the base for relative URLs.
+///
+/// After creation, this URL may be used to get the key for a
+/// module in the binary.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
+pub struct StandaloneRelativeFileBaseUrl<'a>(&'a Url);
+
+impl<'a> From<&'a Url> for StandaloneRelativeFileBaseUrl<'a> {
+  fn from(url: &'a Url) -> Self {
+    Self(url)
+  }
+}
+
+impl<'a> StandaloneRelativeFileBaseUrl<'a> {
+  pub fn new(url: &'a Url) -> Self {
+    debug_assert_eq!(url.scheme(), "file");
+    Self(url)
+  }
+
+  /// Gets the module map key of the provided specifier.
+  ///
+  /// * Descendant file specifiers will be made relative to the base.
+  /// * Non-descendant file specifiers will stay as-is (absolute).
+  /// * Non-file specifiers will stay as-is.
+  pub fn specifier_key<'b>(&self, target: &'b Url) -> Cow<'b, str> {
+    if target.scheme() != "file" {
+      return Cow::Borrowed(target.as_str());
+    }
+
+    match self.0.make_relative(target) {
+      Some(relative) => {
+        if relative.starts_with("../") {
+          Cow::Borrowed(target.as_str())
+        } else {
+          Cow::Owned(relative)
+        }
+      }
+      None => Cow::Borrowed(target.as_str()),
+    }
+  }
+
+  pub fn inner(&self) -> &Url {
+    self.0
+  }
+}
 
 #[derive(Deserialize, Serialize)]
 pub enum NodeModules {
@@ -120,78 +185,23 @@ pub struct Metadata {
   pub unstable_config: UnstableConfig,
 }
 
-pub fn load_npm_vfs(root_dir_path: PathBuf) -> Result<FileBackedVfs, AnyError> {
-  let data = libsui::find_section("d3n0l4nd").unwrap();
-
-  // We do the first part sync so it can complete quickly
-  let trailer: [u8; TRAILER_SIZE] = data[0..TRAILER_SIZE].try_into().unwrap();
-  let trailer = match Trailer::parse(&trailer)? {
-    None => panic!("Could not find trailer"),
-    Some(trailer) => trailer,
-  };
-  let data = &data[TRAILER_SIZE..];
-
-  let vfs_data =
-    &data[trailer.npm_vfs_pos as usize..trailer.npm_files_pos as usize];
-  let mut dir: VirtualDirectory = serde_json::from_slice(vfs_data)?;
-
-  // align the name of the directory with the root dir
-  dir.name = root_dir_path
-    .file_name()
-    .unwrap()
-    .to_string_lossy()
-    .to_string();
-
-  let fs_root = VfsRoot {
-    dir,
-    root_path: root_dir_path,
-    start_file_offset: trailer.npm_files_pos,
-  };
-  Ok(FileBackedVfs::new(data.to_vec(), fs_root))
-}
-
 fn write_binary_bytes(
   mut file_writer: File,
   original_bin: Vec<u8>,
   metadata: &Metadata,
-  eszip: eszip::EszipV2,
-  npm_vfs: Option<&VirtualDirectory>,
-  npm_files: &Vec<Vec<u8>>,
+  npm_snapshot: Option<SerializedNpmResolutionSnapshot>,
+  remote_modules: &RemoteModulesStoreBuilder,
+  vfs: VfsBuilder,
   compile_flags: &CompileFlags,
 ) -> Result<(), AnyError> {
-  let metadata = serde_json::to_string(metadata)?.as_bytes().to_vec();
-  let npm_vfs = serde_json::to_string(&npm_vfs)?.as_bytes().to_vec();
-  let eszip_archive = eszip.into_bytes();
-
-  let mut writer = Vec::new();
-
-  // write the trailer, which includes the positions
-  // of the data blocks in the file
-  writer.write_all(&{
-    let metadata_pos = eszip_archive.len() as u64;
-    let npm_vfs_pos = metadata_pos + (metadata.len() as u64);
-    let npm_files_pos = npm_vfs_pos + (npm_vfs.len() as u64);
-    Trailer {
-      eszip_pos: 0,
-      metadata_pos,
-      npm_vfs_pos,
-      npm_files_pos,
-    }
-    .as_bytes()
-  })?;
-
-  writer.write_all(&eszip_archive)?;
-  writer.write_all(&metadata)?;
-  writer.write_all(&npm_vfs)?;
-  for file in npm_files {
-    writer.write_all(file)?;
-  }
+  let data_section_bytes =
+    serialize_binary_data_section(metadata, npm_snapshot, remote_modules, vfs)?;
 
   let target = compile_flags.resolve_target();
   if target.contains("linux") {
     libsui::Elf::new(&original_bin).append(
       "d3n0l4nd",
-      &writer,
+      &data_section_bytes,
       &mut file_writer,
     )?;
   } else if target.contains("windows") {
@@ -201,11 +211,11 @@ fn write_binary_bytes(
       pe = pe.set_icon(&icon)?;
     }
 
-    pe.write_resource("d3n0l4nd", writer)?
+    pe.write_resource("d3n0l4nd", data_section_bytes)?
       .build(&mut file_writer)?;
   } else if target.contains("darwin") {
     libsui::Macho::from(original_bin)?
-      .write_section("d3n0l4nd", writer)?
+      .write_section("d3n0l4nd", data_section_bytes)?
       .build_and_sign(&mut file_writer)?;
   }
   Ok(())
@@ -221,6 +231,63 @@ pub fn is_standalone_binary(exe_path: &Path) -> bool {
     || libsui::utils::is_macho(&data)
 }
 
+pub struct StandaloneData {
+  pub fs: Arc<dyn deno_fs::FileSystem>,
+  pub metadata: Metadata,
+  pub modules: StandaloneModules,
+  pub npm_snapshot: Option<ValidSerializedNpmResolutionSnapshot>,
+  pub root_path: PathBuf,
+  pub vfs: Arc<FileBackedVfs>,
+}
+
+pub struct StandaloneModules {
+  remote_modules: RemoteModulesStore,
+  vfs: Arc<FileBackedVfs>,
+}
+
+impl StandaloneModules {
+  pub fn resolve_specifier<'a>(
+    &'a self,
+    specifier: &'a ModuleSpecifier,
+  ) -> Result<Option<&'a ModuleSpecifier>, AnyError> {
+    if specifier.scheme() == "file" {
+      Ok(Some(specifier))
+    } else {
+      self.remote_modules.resolve_specifier(specifier)
+    }
+  }
+
+  pub fn read<'a>(
+    &'a self,
+    specifier: &'a ModuleSpecifier,
+  ) -> Result<Option<DenoCompileModuleData<'a>>, AnyError> {
+    if specifier.scheme() == "file" {
+      let path = deno_path_util::url_to_file_path(specifier)?;
+      let bytes = match self.vfs.file_entry(&path) {
+        Ok(entry) => self.vfs.read_file_all(entry)?,
+        Err(err) if err.kind() == ErrorKind::NotFound => {
+          let bytes = match RealFs.read_file_sync(&path, None) {
+            Ok(bytes) => bytes,
+            Err(FsError::Io(err)) if err.kind() == ErrorKind::NotFound => {
+              return Ok(None)
+            }
+            Err(err) => return Err(err.into()),
+          };
+          Cow::Owned(bytes)
+        }
+        Err(err) => return Err(err.into()),
+      };
+      Ok(Some(DenoCompileModuleData {
+        media_type: MediaType::from_specifier(specifier),
+        specifier,
+        data: bytes,
+      }))
+    } else {
+      self.remote_modules.read(specifier)
+    }
+  }
+}
+
 /// This function will try to run this binary as a standalone binary
 /// produced by `deno compile`. It determines if this is a standalone
 /// binary by skipping over the trailer width at the end of the file,
@@ -228,110 +295,66 @@ pub fn is_standalone_binary(exe_path: &Path) -> bool {
 /// the bundle is executed. If not, this function exits with `Ok(None)`.
 pub fn extract_standalone(
   cli_args: Cow<Vec<OsString>>,
-) -> Result<
-  Option<impl Future<Output = Result<(Metadata, eszip::EszipV2), AnyError>>>,
-  AnyError,
-> {
+) -> Result<Option<StandaloneData>, AnyError> {
   let Some(data) = libsui::find_section("d3n0l4nd") else {
     return Ok(None);
   };
 
-  // We do the first part sync so it can complete quickly
-  let trailer = match Trailer::parse(&data[0..TRAILER_SIZE])? {
+  let DeserializedDataSection {
+    mut metadata,
+    npm_snapshot,
+    remote_modules,
+    mut vfs_dir,
+    vfs_files_data,
+  } = match deserialize_binary_data_section(data)? {
+    Some(data_section) => data_section,
     None => return Ok(None),
-    Some(trailer) => trailer,
   };
 
+  let root_path = {
+    let maybe_current_exe = std::env::current_exe().ok();
+    let current_exe_name = maybe_current_exe
+      .as_ref()
+      .and_then(|p| p.file_name())
+      .map(|p| p.to_string_lossy())
+      // should never happen
+      .unwrap_or_else(|| Cow::Borrowed("binary"));
+    std::env::temp_dir().join(format!("deno-compile-{}", current_exe_name))
+  };
   let cli_args = cli_args.into_owned();
-  // If we have an eszip, read it out
-  Ok(Some(async move {
-    let bufreader =
-      deno_core::futures::io::BufReader::new(&data[TRAILER_SIZE..]);
+  metadata.argv.reserve(cli_args.len() - 1);
+  for arg in cli_args.into_iter().skip(1) {
+    metadata.argv.push(arg.into_string().unwrap());
+  }
+  let vfs = {
+    // align the name of the directory with the root dir
+    vfs_dir.name = root_path.file_name().unwrap().to_string_lossy().to_string();
 
-    let (eszip, loader) = eszip::EszipV2::parse(bufreader)
-      .await
-      .context("Failed to parse eszip header")?;
-
-    let bufreader = loader.await.context("Failed to parse eszip archive")?;
-
-    let mut metadata = String::new();
-
-    bufreader
-      .take(trailer.metadata_len())
-      .read_to_string(&mut metadata)
-      .await
-      .context("Failed to read metadata from the current executable")?;
-
-    let mut metadata: Metadata = serde_json::from_str(&metadata).unwrap();
-    metadata.argv.reserve(cli_args.len() - 1);
-    for arg in cli_args.into_iter().skip(1) {
-      metadata.argv.push(arg.into_string().unwrap());
-    }
-
-    Ok((metadata, eszip))
+    let fs_root = VfsRoot {
+      dir: vfs_dir,
+      root_path: root_path.clone(),
+      start_file_offset: 0,
+    };
+    Arc::new(FileBackedVfs::new(Cow::Borrowed(vfs_files_data), fs_root))
+  };
+  let fs: Arc<dyn deno_fs::FileSystem> =
+    Arc::new(DenoCompileFileSystem::new(vfs.clone()));
+  Ok(Some(StandaloneData {
+    fs,
+    metadata,
+    modules: StandaloneModules {
+      remote_modules,
+      vfs: vfs.clone(),
+    },
+    npm_snapshot,
+    root_path,
+    vfs,
   }))
 }
 
-const TRAILER_SIZE: usize = std::mem::size_of::<Trailer>() + 8; // 8 bytes for the magic trailer string
-
-struct Trailer {
-  eszip_pos: u64,
-  metadata_pos: u64,
-  npm_vfs_pos: u64,
-  npm_files_pos: u64,
-}
-
-impl Trailer {
-  pub fn parse(trailer: &[u8]) -> Result<Option<Trailer>, AnyError> {
-    let (magic_trailer, rest) = trailer.split_at(8);
-    if magic_trailer != MAGIC_TRAILER {
-      return Ok(None);
-    }
-
-    let (eszip_archive_pos, rest) = rest.split_at(8);
-    let (metadata_pos, rest) = rest.split_at(8);
-    let (npm_vfs_pos, npm_files_pos) = rest.split_at(8);
-    let eszip_archive_pos = u64_from_bytes(eszip_archive_pos)?;
-    let metadata_pos = u64_from_bytes(metadata_pos)?;
-    let npm_vfs_pos = u64_from_bytes(npm_vfs_pos)?;
-    let npm_files_pos = u64_from_bytes(npm_files_pos)?;
-    Ok(Some(Trailer {
-      eszip_pos: eszip_archive_pos,
-      metadata_pos,
-      npm_vfs_pos,
-      npm_files_pos,
-    }))
-  }
-
-  pub fn metadata_len(&self) -> u64 {
-    self.npm_vfs_pos - self.metadata_pos
-  }
-
-  pub fn npm_vfs_len(&self) -> u64 {
-    self.npm_files_pos - self.npm_vfs_pos
-  }
-
-  pub fn as_bytes(&self) -> Vec<u8> {
-    let mut trailer = MAGIC_TRAILER.to_vec();
-    trailer.write_all(&self.eszip_pos.to_be_bytes()).unwrap();
-    trailer.write_all(&self.metadata_pos.to_be_bytes()).unwrap();
-    trailer.write_all(&self.npm_vfs_pos.to_be_bytes()).unwrap();
-    trailer
-      .write_all(&self.npm_files_pos.to_be_bytes())
-      .unwrap();
-    trailer
-  }
-}
-
-fn u64_from_bytes(arr: &[u8]) -> Result<u64, AnyError> {
-  let fixed_arr: &[u8; 8] = arr
-    .try_into()
-    .context("Failed to convert the buffer into a fixed-size array")?;
-  Ok(u64::from_be_bytes(*fixed_arr))
-}
-
 pub struct DenoCompileBinaryWriter<'a> {
   deno_dir: &'a DenoDir,
+  emitter: &'a Emitter,
   file_fetcher: &'a FileFetcher,
   http_client_provider: &'a HttpClientProvider,
   npm_resolver: &'a dyn CliNpmResolver,
@@ -343,6 +366,7 @@ impl<'a> DenoCompileBinaryWriter<'a> {
   #[allow(clippy::too_many_arguments)]
   pub fn new(
     deno_dir: &'a DenoDir,
+    emitter: &'a Emitter,
     file_fetcher: &'a FileFetcher,
     http_client_provider: &'a HttpClientProvider,
     npm_resolver: &'a dyn CliNpmResolver,
@@ -351,6 +375,7 @@ impl<'a> DenoCompileBinaryWriter<'a> {
   ) -> Self {
     Self {
       deno_dir,
+      emitter,
       file_fetcher,
       http_client_provider,
       npm_resolver,
@@ -362,8 +387,8 @@ impl<'a> DenoCompileBinaryWriter<'a> {
   pub async fn write_bin(
     &self,
     writer: File,
-    eszip: eszip::EszipV2,
-    root_dir_url: EszipRelativeFileBaseUrl<'_>,
+    graph: &ModuleGraph,
+    root_dir_url: StandaloneRelativeFileBaseUrl<'_>,
     entrypoint: &ModuleSpecifier,
     compile_flags: &CompileFlags,
     cli_options: &CliOptions,
@@ -390,15 +415,17 @@ impl<'a> DenoCompileBinaryWriter<'a> {
         )
       }
     }
-    self.write_standalone_binary(
-      writer,
-      original_binary,
-      eszip,
-      root_dir_url,
-      entrypoint,
-      cli_options,
-      compile_flags,
-    )
+    self
+      .write_standalone_binary(
+        writer,
+        original_binary,
+        graph,
+        root_dir_url,
+        entrypoint,
+        cli_options,
+        compile_flags,
+      )
+      .await
   }
 
   async fn get_base_binary(
@@ -493,12 +520,12 @@ impl<'a> DenoCompileBinaryWriter<'a> {
   /// This functions creates a standalone deno binary by appending a bundle
   /// and magic trailer to the currently executing binary.
   #[allow(clippy::too_many_arguments)]
-  fn write_standalone_binary(
+  async fn write_standalone_binary(
     &self,
     writer: File,
     original_bin: Vec<u8>,
-    mut eszip: eszip::EszipV2,
-    root_dir_url: EszipRelativeFileBaseUrl<'_>,
+    graph: &ModuleGraph,
+    root_dir_url: StandaloneRelativeFileBaseUrl<'_>,
     entrypoint: &ModuleSpecifier,
     cli_options: &CliOptions,
     compile_flags: &CompileFlags,
@@ -512,19 +539,17 @@ impl<'a> DenoCompileBinaryWriter<'a> {
       None => None,
     };
     let root_path = root_dir_url.inner().to_file_path().unwrap();
-    let (npm_vfs, npm_files, node_modules) = match self.npm_resolver.as_inner()
+    let (maybe_npm_vfs, node_modules, npm_snapshot) = match self
+      .npm_resolver
+      .as_inner()
     {
       InnerCliNpmResolverRef::Managed(managed) => {
         let snapshot =
           managed.serialized_valid_snapshot_for_system(&self.npm_system_info);
         if !snapshot.as_serialized().packages.is_empty() {
-          let (root_dir, files) = self
-            .build_vfs(&root_path, cli_options)?
-            .into_dir_and_files();
-          eszip.add_npm_snapshot(snapshot);
+          let npm_vfs_builder = self.build_npm_vfs(&root_path, cli_options)?;
           (
-            Some(root_dir),
-            files,
+            Some(npm_vfs_builder),
             Some(NodeModules::Managed {
               node_modules_dir: self.npm_resolver.root_node_modules_path().map(
                 |path| {
@@ -536,18 +561,16 @@ impl<'a> DenoCompileBinaryWriter<'a> {
                 },
               ),
             }),
+            Some(snapshot),
           )
         } else {
-          (None, Vec::new(), None)
+          (None, None, None)
         }
       }
       InnerCliNpmResolverRef::Byonm(resolver) => {
-        let (root_dir, files) = self
-          .build_vfs(&root_path, cli_options)?
-          .into_dir_and_files();
+        let npm_vfs_builder = self.build_npm_vfs(&root_path, cli_options)?;
         (
-          Some(root_dir),
-          files,
+          Some(npm_vfs_builder),
           Some(NodeModules::Byonm {
             root_node_modules_dir: resolver.root_node_modules_path().map(
               |node_modules_dir| {
@@ -560,9 +583,67 @@ impl<'a> DenoCompileBinaryWriter<'a> {
               },
             ),
           }),
+          None,
         )
       }
     };
+    let mut vfs = if let Some(npm_vfs) = maybe_npm_vfs {
+      npm_vfs
+    } else {
+      VfsBuilder::new(root_path.clone())?
+    };
+    let mut remote_modules_store = RemoteModulesStoreBuilder::default();
+    for module in graph.modules() {
+      if module.specifier().scheme() == "data" {
+        continue; // don't store data urls as an entry as they're in the code
+      }
+      let (maybe_source, media_type) = match module {
+        deno_graph::Module::Js(m) => {
+          // todo(https://github.com/denoland/deno_media_type/pull/12): use is_emittable()
+          let is_emittable = matches!(
+            m.media_type,
+            MediaType::TypeScript
+              | MediaType::Mts
+              | MediaType::Cts
+              | MediaType::Jsx
+              | MediaType::Tsx
+          );
+          let source = if is_emittable {
+            let source = self
+              .emitter
+              .emit_parsed_source(&m.specifier, m.media_type, &m.source)
+              .await?;
+            source.to_vec()
+          } else {
+            m.source.as_bytes().to_vec()
+          };
+          (Some(source), m.media_type)
+        }
+        deno_graph::Module::Json(m) => {
+          (Some(m.source.as_bytes().to_vec()), m.media_type)
+        }
+        deno_graph::Module::Npm(_)
+        | deno_graph::Module::Node(_)
+        | deno_graph::Module::External(_) => (None, MediaType::Unknown),
+      };
+      if module.specifier().scheme() == "file" {
+        let file_path = deno_path_util::url_to_file_path(module.specifier())?;
+        vfs
+          .add_file_with_data(
+            &file_path,
+            match maybe_source {
+              Some(source) => source,
+              None => RealFs.read_file_sync(&file_path, None)?,
+            },
+          )
+          .with_context(|| {
+            format!("Failed adding '{}'", file_path.display())
+          })?;
+      } else if let Some(source) = maybe_source {
+        remote_modules_store.add(module.specifier(), media_type, source);
+      }
+    }
+    remote_modules_store.add_redirects(&graph.redirects);
 
     let env_vars_from_env_file = match cli_options.env_file_name() {
       Some(env_filename) => {
@@ -636,14 +717,14 @@ impl<'a> DenoCompileBinaryWriter<'a> {
       writer,
       original_bin,
       &metadata,
-      eszip,
-      npm_vfs.as_ref(),
-      &npm_files,
+      npm_snapshot.map(|s| s.into_serialized()),
+      &remote_modules_store,
+      vfs,
       compile_flags,
     )
   }
 
-  fn build_vfs(
+  fn build_npm_vfs(
     &self,
     root_path: &Path,
     cli_options: &CliOptions,
@@ -664,8 +745,8 @@ impl<'a> DenoCompileBinaryWriter<'a> {
         } else {
           // DO NOT include the user's registry url as it may contain credentials,
           // but also don't make this dependent on the registry url
-          let root_path = npm_resolver.global_cache_root_folder();
-          let mut builder = VfsBuilder::new(root_path)?;
+          let global_cache_root_path = npm_resolver.global_cache_root_folder();
+          let mut builder = VfsBuilder::new(global_cache_root_path)?;
           let mut packages =
             npm_resolver.all_system_packages(&self.npm_system_info);
           packages.sort_by(|a, b| a.id.cmp(&b.id)); // determinism
@@ -675,12 +756,12 @@ impl<'a> DenoCompileBinaryWriter<'a> {
             builder.add_dir_recursive(&folder)?;
           }
 
-          // Flatten all the registries folders into a single "node_modules/localhost" folder
+          // Flatten all the registries folders into a single ".deno_compile_node_modules/localhost" folder
           // that will be used by denort when loading the npm cache. This avoids us exposing
           // the user's private registry information and means we don't have to bother
           // serializing all the different registry config into the binary.
           builder.with_root_dir(|root_dir| {
-            root_dir.name = "node_modules".to_string();
+            root_dir.name = ".deno_compile_node_modules".to_string();
             let mut new_entries = Vec::with_capacity(root_dir.entries.len());
             let mut localhost_entries = IndexMap::new();
             for entry in std::mem::take(&mut root_dir.entries) {
@@ -715,6 +796,8 @@ impl<'a> DenoCompileBinaryWriter<'a> {
             root_dir.entries = new_entries;
           });
 
+          builder.set_new_root_path(root_path.to_path_buf())?;
+
           Ok(builder)
         }
       }
diff --git a/cli/standalone/file_system.rs b/cli/standalone/file_system.rs
index 314444630b..712c6ee918 100644
--- a/cli/standalone/file_system.rs
+++ b/cli/standalone/file_system.rs
@@ -22,8 +22,8 @@ use super::virtual_fs::FileBackedVfs;
 pub struct DenoCompileFileSystem(Arc<FileBackedVfs>);
 
 impl DenoCompileFileSystem {
-  pub fn new(vfs: FileBackedVfs) -> Self {
-    Self(Arc::new(vfs))
+  pub fn new(vfs: Arc<FileBackedVfs>) -> Self {
+    Self(vfs)
   }
 
   fn error_if_in_vfs(&self, path: &Path) -> FsResult<()> {
diff --git a/cli/standalone/mod.rs b/cli/standalone/mod.rs
index 60018228b7..3a62b6ff96 100644
--- a/cli/standalone/mod.rs
+++ b/cli/standalone/mod.rs
@@ -5,6 +5,8 @@
 #![allow(dead_code)]
 #![allow(unused_imports)]
 
+use binary::StandaloneData;
+use binary::StandaloneModules;
 use deno_ast::MediaType;
 use deno_cache_dir::npm::NpmCacheDir;
 use deno_config::workspace::MappedResolution;
@@ -38,7 +40,6 @@ use deno_runtime::permissions::RuntimePermissionDescriptorParser;
 use deno_runtime::WorkerExecutionMode;
 use deno_runtime::WorkerLogLevel;
 use deno_semver::npm::NpmPackageReqReference;
-use eszip::EszipRelativeFileBaseUrl;
 use import_map::parse_from_json;
 use node_resolver::analyze::NodeCodeTranslator;
 use node_resolver::NodeResolutionMode;
@@ -54,6 +55,7 @@ use crate::args::CacheSetting;
 use crate::args::NpmInstallDepsProvider;
 use crate::args::StorageKeyResolver;
 use crate::cache::Caches;
+use crate::cache::DenoCacheEnvFsAdapter;
 use crate::cache::DenoDirProvider;
 use crate::cache::NodeAnalysisCache;
 use crate::cache::RealDenoCacheEnv;
@@ -78,52 +80,18 @@ use crate::worker::ModuleLoaderFactory;
 
 pub mod binary;
 mod file_system;
+mod serialization;
 mod virtual_fs;
 
 pub use binary::extract_standalone;
 pub use binary::is_standalone_binary;
 pub use binary::DenoCompileBinaryWriter;
 
-use self::binary::load_npm_vfs;
 use self::binary::Metadata;
 use self::file_system::DenoCompileFileSystem;
 
-struct WorkspaceEszipModule {
-  specifier: ModuleSpecifier,
-  inner: eszip::Module,
-}
-
-struct WorkspaceEszip {
-  eszip: eszip::EszipV2,
-  root_dir_url: Arc<ModuleSpecifier>,
-}
-
-impl WorkspaceEszip {
-  pub fn get_module(
-    &self,
-    specifier: &ModuleSpecifier,
-  ) -> Option<WorkspaceEszipModule> {
-    if specifier.scheme() == "file" {
-      let specifier_key = EszipRelativeFileBaseUrl::new(&self.root_dir_url)
-        .specifier_key(specifier);
-      let module = self.eszip.get_module(&specifier_key)?;
-      let specifier = self.root_dir_url.join(&module.specifier).unwrap();
-      Some(WorkspaceEszipModule {
-        specifier,
-        inner: module,
-      })
-    } else {
-      let module = self.eszip.get_module(specifier.as_str())?;
-      Some(WorkspaceEszipModule {
-        specifier: ModuleSpecifier::parse(&module.specifier).unwrap(),
-        inner: module,
-      })
-    }
-  }
-}
-
 struct SharedModuleLoaderState {
-  eszip: WorkspaceEszip,
+  modules: StandaloneModules,
   workspace_resolver: WorkspaceResolver,
   node_resolver: Arc<CliNodeResolver>,
   npm_module_loader: Arc<NpmModuleLoader>,
@@ -249,8 +217,10 @@ impl ModuleLoader for EmbeddedModuleLoader {
         }
 
         if specifier.scheme() == "jsr" {
-          if let Some(module) = self.shared.eszip.get_module(&specifier) {
-            return Ok(module.specifier);
+          if let Some(specifier) =
+            self.shared.modules.resolve_specifier(&specifier)?
+          {
+            return Ok(specifier.clone());
           }
         }
 
@@ -345,56 +315,30 @@ impl ModuleLoader for EmbeddedModuleLoader {
       );
     }
 
-    let Some(module) = self.shared.eszip.get_module(original_specifier) else {
-      return deno_core::ModuleLoadResponse::Sync(Err(type_error(format!(
-        "{MODULE_NOT_FOUND}: {}",
-        original_specifier
-      ))));
-    };
-    let original_specifier = original_specifier.clone();
-
-    deno_core::ModuleLoadResponse::Async(
-      async move {
-        let code = module.inner.source().await.ok_or_else(|| {
-          type_error(format!("Module not found: {}", original_specifier))
-        })?;
-        let code = arc_u8_to_arc_str(code)
-          .map_err(|_| type_error("Module source is not utf-8"))?;
-        Ok(deno_core::ModuleSource::new_with_redirect(
-          match module.inner.kind {
-            eszip::ModuleKind::JavaScript => ModuleType::JavaScript,
-            eszip::ModuleKind::Json => ModuleType::Json,
-            eszip::ModuleKind::Jsonc => {
-              return Err(type_error("jsonc modules not supported"))
-            }
-            eszip::ModuleKind::OpaqueData => {
-              unreachable!();
-            }
-          },
-          ModuleSourceCode::String(code.into()),
-          &original_specifier,
-          &module.specifier,
-          None,
+    match self.shared.modules.read(original_specifier) {
+      Ok(Some(module)) => {
+        let (module_specifier, module_type, module_source) =
+          module.into_for_v8();
+        deno_core::ModuleLoadResponse::Sync(Ok(
+          deno_core::ModuleSource::new_with_redirect(
+            module_type,
+            module_source,
+            original_specifier,
+            module_specifier,
+            None,
+          ),
         ))
       }
-      .boxed_local(),
-    )
+      Ok(None) => deno_core::ModuleLoadResponse::Sync(Err(type_error(
+        format!("{MODULE_NOT_FOUND}: {}", original_specifier),
+      ))),
+      Err(err) => deno_core::ModuleLoadResponse::Sync(Err(type_error(
+        format!("{:?}", err),
+      ))),
+    }
   }
 }
 
-fn arc_u8_to_arc_str(
-  arc_u8: Arc<[u8]>,
-) -> Result<Arc<str>, std::str::Utf8Error> {
-  // Check that the string is valid UTF-8.
-  std::str::from_utf8(&arc_u8)?;
-  // SAFETY: the string is valid UTF-8, and the layout Arc<[u8]> is the same as
-  // Arc<str>. This is proven by the From<Arc<str>> impl for Arc<[u8]> from the
-  // standard library.
-  Ok(unsafe {
-    std::mem::transmute::<std::sync::Arc<[u8]>, std::sync::Arc<str>>(arc_u8)
-  })
-}
-
 struct StandaloneModuleLoaderFactory {
   shared: Arc<SharedModuleLoaderState>,
 }
@@ -439,13 +383,15 @@ impl RootCertStoreProvider for StandaloneRootCertStoreProvider {
   }
 }
 
-pub async fn run(
-  mut eszip: eszip::EszipV2,
-  metadata: Metadata,
-) -> Result<i32, AnyError> {
-  let current_exe_path = std::env::current_exe().unwrap();
-  let current_exe_name =
-    current_exe_path.file_name().unwrap().to_string_lossy();
+pub async fn run(data: StandaloneData) -> Result<i32, AnyError> {
+  let StandaloneData {
+    fs,
+    metadata,
+    modules,
+    npm_snapshot,
+    root_path,
+    vfs,
+  } = data;
   let deno_dir_provider = Arc::new(DenoDirProvider::new(None));
   let root_cert_store_provider = Arc::new(StandaloneRootCertStoreProvider {
     ca_stores: metadata.ca_stores,
@@ -459,112 +405,83 @@ pub async fn run(
   ));
   // use a dummy npm registry url
   let npm_registry_url = ModuleSpecifier::parse("https://localhost/").unwrap();
-  let root_path =
-    std::env::temp_dir().join(format!("deno-compile-{}", current_exe_name));
   let root_dir_url =
     Arc::new(ModuleSpecifier::from_directory_path(&root_path).unwrap());
   let main_module = root_dir_url.join(&metadata.entrypoint_key).unwrap();
-  let root_node_modules_path = root_path.join("node_modules");
-  let npm_cache_dir = NpmCacheDir::new(
-    &RealDenoCacheEnv,
-    root_node_modules_path.clone(),
-    vec![npm_registry_url.clone()],
-  );
-  let npm_global_cache_dir = npm_cache_dir.get_cache_location();
+  let npm_global_cache_dir = root_path.join(".deno_compile_node_modules");
   let cache_setting = CacheSetting::Only;
-  let (fs, npm_resolver, maybe_vfs_root) = match metadata.node_modules {
+  let npm_resolver = match metadata.node_modules {
     Some(binary::NodeModules::Managed { node_modules_dir }) => {
-      // this will always have a snapshot
-      let snapshot = eszip.take_npm_snapshot().unwrap();
-      let vfs_root_dir_path = if node_modules_dir.is_some() {
-        root_path.clone()
-      } else {
-        npm_cache_dir.root_dir().to_owned()
-      };
-      let vfs = load_npm_vfs(vfs_root_dir_path.clone())
-        .context("Failed to load npm vfs.")?;
+      let snapshot = npm_snapshot.unwrap();
       let maybe_node_modules_path = node_modules_dir
-        .map(|node_modules_dir| vfs_root_dir_path.join(node_modules_dir));
-      let fs = Arc::new(DenoCompileFileSystem::new(vfs))
-        as Arc<dyn deno_fs::FileSystem>;
-      let npm_resolver =
-        create_cli_npm_resolver(CliNpmResolverCreateOptions::Managed(
-          CliNpmResolverManagedCreateOptions {
-            snapshot: CliNpmResolverManagedSnapshotOption::Specified(Some(
-              snapshot,
-            )),
-            maybe_lockfile: None,
-            fs: fs.clone(),
-            http_client_provider: http_client_provider.clone(),
-            npm_global_cache_dir,
-            cache_setting,
-            text_only_progress_bar: progress_bar,
-            maybe_node_modules_path,
-            npm_system_info: Default::default(),
-            npm_install_deps_provider: Arc::new(
-              // this is only used for installing packages, which isn't necessary with deno compile
-              NpmInstallDepsProvider::empty(),
-            ),
-            // create an npmrc that uses the fake npm_registry_url to resolve packages
-            npmrc: Arc::new(ResolvedNpmRc {
-              default_config: deno_npm::npm_rc::RegistryConfigWithUrl {
-                registry_url: npm_registry_url.clone(),
-                config: Default::default(),
-              },
-              scopes: Default::default(),
-              registry_configs: Default::default(),
-            }),
-            lifecycle_scripts: Default::default(),
-          },
-        ))
-        .await?;
-      (fs, npm_resolver, Some(vfs_root_dir_path))
+        .map(|node_modules_dir| root_path.join(node_modules_dir));
+      create_cli_npm_resolver(CliNpmResolverCreateOptions::Managed(
+        CliNpmResolverManagedCreateOptions {
+          snapshot: CliNpmResolverManagedSnapshotOption::Specified(Some(
+            snapshot,
+          )),
+          maybe_lockfile: None,
+          fs: fs.clone(),
+          http_client_provider: http_client_provider.clone(),
+          npm_global_cache_dir,
+          cache_setting,
+          text_only_progress_bar: progress_bar,
+          maybe_node_modules_path,
+          npm_system_info: Default::default(),
+          npm_install_deps_provider: Arc::new(
+            // this is only used for installing packages, which isn't necessary with deno compile
+            NpmInstallDepsProvider::empty(),
+          ),
+          // create an npmrc that uses the fake npm_registry_url to resolve packages
+          npmrc: Arc::new(ResolvedNpmRc {
+            default_config: deno_npm::npm_rc::RegistryConfigWithUrl {
+              registry_url: npm_registry_url.clone(),
+              config: Default::default(),
+            },
+            scopes: Default::default(),
+            registry_configs: Default::default(),
+          }),
+          lifecycle_scripts: Default::default(),
+        },
+      ))
+      .await?
     }
     Some(binary::NodeModules::Byonm {
       root_node_modules_dir,
     }) => {
-      let vfs_root_dir_path = root_path.clone();
-      let vfs = load_npm_vfs(vfs_root_dir_path.clone())
-        .context("Failed to load vfs.")?;
       let root_node_modules_dir =
         root_node_modules_dir.map(|p| vfs.root().join(p));
-      let fs = Arc::new(DenoCompileFileSystem::new(vfs))
-        as Arc<dyn deno_fs::FileSystem>;
-      let npm_resolver = create_cli_npm_resolver(
-        CliNpmResolverCreateOptions::Byonm(CliByonmNpmResolverCreateOptions {
+      create_cli_npm_resolver(CliNpmResolverCreateOptions::Byonm(
+        CliByonmNpmResolverCreateOptions {
           fs: CliDenoResolverFs(fs.clone()),
           root_node_modules_dir,
-        }),
-      )
-      .await?;
-      (fs, npm_resolver, Some(vfs_root_dir_path))
+        },
+      ))
+      .await?
     }
     None => {
-      let fs = Arc::new(deno_fs::RealFs) as Arc<dyn deno_fs::FileSystem>;
-      let npm_resolver =
-        create_cli_npm_resolver(CliNpmResolverCreateOptions::Managed(
-          CliNpmResolverManagedCreateOptions {
-            snapshot: CliNpmResolverManagedSnapshotOption::Specified(None),
-            maybe_lockfile: None,
-            fs: fs.clone(),
-            http_client_provider: http_client_provider.clone(),
-            npm_global_cache_dir,
-            cache_setting,
-            text_only_progress_bar: progress_bar,
-            maybe_node_modules_path: None,
-            npm_system_info: Default::default(),
-            npm_install_deps_provider: Arc::new(
-              // this is only used for installing packages, which isn't necessary with deno compile
-              NpmInstallDepsProvider::empty(),
-            ),
-            // Packages from different registries are already inlined in the ESZip,
-            // so no need to create actual `.npmrc` configuration.
-            npmrc: create_default_npmrc(),
-            lifecycle_scripts: Default::default(),
-          },
-        ))
-        .await?;
-      (fs, npm_resolver, None)
+      create_cli_npm_resolver(CliNpmResolverCreateOptions::Managed(
+        CliNpmResolverManagedCreateOptions {
+          snapshot: CliNpmResolverManagedSnapshotOption::Specified(None),
+          maybe_lockfile: None,
+          fs: fs.clone(),
+          http_client_provider: http_client_provider.clone(),
+          npm_global_cache_dir,
+          cache_setting,
+          text_only_progress_bar: progress_bar,
+          maybe_node_modules_path: None,
+          npm_system_info: Default::default(),
+          npm_install_deps_provider: Arc::new(
+            // this is only used for installing packages, which isn't necessary with deno compile
+            NpmInstallDepsProvider::empty(),
+          ),
+          // Packages from different registries are already inlined in the binary,
+          // so no need to create actual `.npmrc` configuration.
+          npmrc: create_default_npmrc(),
+          lifecycle_scripts: Default::default(),
+        },
+      ))
+      .await?
     }
   };
 
@@ -645,10 +562,7 @@ pub async fn run(
   };
   let module_loader_factory = StandaloneModuleLoaderFactory {
     shared: Arc::new(SharedModuleLoaderState {
-      eszip: WorkspaceEszip {
-        eszip,
-        root_dir_url,
-      },
+      modules,
       workspace_resolver,
       node_resolver: cli_node_resolver.clone(),
       npm_module_loader: Arc::new(NpmModuleLoader::new(
@@ -663,19 +577,17 @@ pub async fn run(
   let permissions = {
     let mut permissions =
       metadata.permissions.to_options(/* cli_arg_urls */ &[]);
-    // if running with an npm vfs, grant read access to it
-    if let Some(vfs_root) = maybe_vfs_root {
-      match &mut permissions.allow_read {
-        Some(vec) if vec.is_empty() => {
-          // do nothing, already granted
-        }
-        Some(vec) => {
-          vec.push(vfs_root.to_string_lossy().to_string());
-        }
-        None => {
-          permissions.allow_read =
-            Some(vec![vfs_root.to_string_lossy().to_string()]);
-        }
+    // grant read access to the vfs
+    match &mut permissions.allow_read {
+      Some(vec) if vec.is_empty() => {
+        // do nothing, already granted
+      }
+      Some(vec) => {
+        vec.push(root_path.to_string_lossy().to_string());
+      }
+      None => {
+        permissions.allow_read =
+          Some(vec![root_path.to_string_lossy().to_string()]);
       }
     }
 
diff --git a/cli/standalone/serialization.rs b/cli/standalone/serialization.rs
new file mode 100644
index 0000000000..12927845bc
--- /dev/null
+++ b/cli/standalone/serialization.rs
@@ -0,0 +1,642 @@
+// Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
+
+use std::borrow::Cow;
+use std::collections::BTreeMap;
+use std::collections::HashMap;
+use std::io::Write;
+
+use deno_ast::MediaType;
+use deno_core::anyhow::bail;
+use deno_core::anyhow::Context;
+use deno_core::error::AnyError;
+use deno_core::serde_json;
+use deno_core::url::Url;
+use deno_core::FastString;
+use deno_core::ModuleSourceCode;
+use deno_core::ModuleType;
+use deno_npm::resolution::SerializedNpmResolutionSnapshot;
+use deno_npm::resolution::SerializedNpmResolutionSnapshotPackage;
+use deno_npm::resolution::ValidSerializedNpmResolutionSnapshot;
+use deno_npm::NpmPackageId;
+use deno_semver::package::PackageReq;
+
+use crate::standalone::virtual_fs::VirtualDirectory;
+
+use super::binary::Metadata;
+use super::virtual_fs::VfsBuilder;
+
+const MAGIC_BYTES: &[u8; 8] = b"d3n0l4nd";
+
+/// Binary format:
+/// * d3n0l4nd
+/// * <metadata_len><metadata>
+/// * <npm_snapshot_len><npm_snapshot>
+/// * <remote_modules_len><remote_modules>
+/// * <vfs_headers_len><vfs_headers>
+/// * <vfs_file_data_len><vfs_file_data>
+/// * d3n0l4nd
+pub fn serialize_binary_data_section(
+  metadata: &Metadata,
+  npm_snapshot: Option<SerializedNpmResolutionSnapshot>,
+  remote_modules: &RemoteModulesStoreBuilder,
+  vfs: VfsBuilder,
+) -> Result<Vec<u8>, AnyError> {
+  fn write_bytes_with_len(bytes: &mut Vec<u8>, data: &[u8]) {
+    bytes.extend_from_slice(&(data.len() as u64).to_le_bytes());
+    bytes.extend_from_slice(data);
+  }
+
+  let mut bytes = Vec::new();
+  bytes.extend_from_slice(MAGIC_BYTES);
+
+  // 1. Metadata
+  {
+    let metadata = serde_json::to_string(metadata)?;
+    write_bytes_with_len(&mut bytes, metadata.as_bytes());
+  }
+  // 2. Npm snapshot
+  {
+    let npm_snapshot =
+      npm_snapshot.map(serialize_npm_snapshot).unwrap_or_default();
+    write_bytes_with_len(&mut bytes, &npm_snapshot);
+  }
+  // 3. Remote modules
+  {
+    let update_index = bytes.len();
+    bytes.extend_from_slice(&(0_u64).to_le_bytes());
+    let start_index = bytes.len();
+    remote_modules.write(&mut bytes)?;
+    let length = bytes.len() - start_index;
+    let length_bytes = (length as u64).to_le_bytes();
+    bytes[update_index..update_index + length_bytes.len()]
+      .copy_from_slice(&length_bytes);
+  }
+  // 4. VFS
+  {
+    let (vfs, vfs_files) = vfs.into_dir_and_files();
+    let vfs = serde_json::to_string(&vfs)?;
+    write_bytes_with_len(&mut bytes, vfs.as_bytes());
+    let vfs_bytes_len = vfs_files.iter().map(|f| f.len() as u64).sum::<u64>();
+    bytes.extend_from_slice(&vfs_bytes_len.to_le_bytes());
+    for file in &vfs_files {
+      bytes.extend_from_slice(file);
+    }
+  }
+
+  // write the magic bytes at the end so we can use it
+  // to make sure we've deserialized correctly
+  bytes.extend_from_slice(MAGIC_BYTES);
+
+  Ok(bytes)
+}
+
+pub struct DeserializedDataSection {
+  pub metadata: Metadata,
+  pub npm_snapshot: Option<ValidSerializedNpmResolutionSnapshot>,
+  pub remote_modules: RemoteModulesStore,
+  pub vfs_dir: VirtualDirectory,
+  pub vfs_files_data: &'static [u8],
+}
+
+pub fn deserialize_binary_data_section(
+  data: &'static [u8],
+) -> Result<Option<DeserializedDataSection>, AnyError> {
+  fn read_bytes_with_len(input: &[u8]) -> Result<(&[u8], &[u8]), AnyError> {
+    let (input, len) = read_u64(input)?;
+    let (input, data) = read_bytes(input, len as usize)?;
+    Ok((input, data))
+  }
+
+  fn read_magic_bytes(input: &[u8]) -> Result<(&[u8], bool), AnyError> {
+    if input.len() < MAGIC_BYTES.len() {
+      bail!("Unexpected end of data. Could not find magic bytes.");
+    }
+    let (magic_bytes, input) = input.split_at(MAGIC_BYTES.len());
+    if magic_bytes != MAGIC_BYTES {
+      return Ok((input, false));
+    }
+    Ok((input, true))
+  }
+
+  let (input, found) = read_magic_bytes(data)?;
+  if !found {
+    return Ok(None);
+  }
+
+  // 1. Metadata
+  let (input, data) = read_bytes_with_len(input).context("reading metadata")?;
+  let metadata: Metadata =
+    serde_json::from_slice(data).context("deserializing metadata")?;
+  // 2. Npm snapshot
+  let (input, data) =
+    read_bytes_with_len(input).context("reading npm snapshot")?;
+  let npm_snapshot = if data.is_empty() {
+    None
+  } else {
+    Some(deserialize_npm_snapshot(data).context("deserializing npm snapshot")?)
+  };
+  // 3. Remote modules
+  let (input, data) =
+    read_bytes_with_len(input).context("reading remote modules data")?;
+  let remote_modules =
+    RemoteModulesStore::build(data).context("deserializing remote modules")?;
+  // 4. VFS
+  let (input, data) = read_bytes_with_len(input).context("vfs")?;
+  let vfs_dir: VirtualDirectory =
+    serde_json::from_slice(data).context("deserializing vfs data")?;
+  let (input, vfs_files_data) =
+    read_bytes_with_len(input).context("reading vfs files data")?;
+
+  // finally ensure we read the magic bytes at the end
+  let (_input, found) = read_magic_bytes(input)?;
+  if !found {
+    bail!("Could not find magic bytes at the end of the data.");
+  }
+
+  Ok(Some(DeserializedDataSection {
+    metadata,
+    npm_snapshot,
+    remote_modules,
+    vfs_dir,
+    vfs_files_data,
+  }))
+}
+
+#[derive(Default)]
+pub struct RemoteModulesStoreBuilder {
+  specifiers: Vec<(String, u64)>,
+  data: Vec<(MediaType, Vec<u8>)>,
+  data_byte_len: u64,
+  redirects: Vec<(String, String)>,
+  redirects_len: u64,
+}
+
+impl RemoteModulesStoreBuilder {
+  pub fn add(&mut self, specifier: &Url, media_type: MediaType, data: Vec<u8>) {
+    let specifier = specifier.to_string();
+    self.specifiers.push((specifier, self.data_byte_len));
+    self.data_byte_len += 1 + 8 + data.len() as u64; // media type (1 byte), data length (8 bytes), data
+    self.data.push((media_type, data));
+  }
+
+  pub fn add_redirects(&mut self, redirects: &BTreeMap<Url, Url>) {
+    self.redirects.reserve(redirects.len());
+    for (from, to) in redirects {
+      let from = from.to_string();
+      let to = to.to_string();
+      self.redirects_len += (4 + from.len() + 4 + to.len()) as u64;
+      self.redirects.push((from, to));
+    }
+  }
+
+  fn write(&self, writer: &mut dyn Write) -> Result<(), AnyError> {
+    writer.write_all(&(self.specifiers.len() as u32).to_le_bytes())?;
+    writer.write_all(&(self.redirects.len() as u32).to_le_bytes())?;
+    for (specifier, offset) in &self.specifiers {
+      writer.write_all(&(specifier.len() as u32).to_le_bytes())?;
+      writer.write_all(specifier.as_bytes())?;
+      writer.write_all(&offset.to_le_bytes())?;
+    }
+    for (from, to) in &self.redirects {
+      writer.write_all(&(from.len() as u32).to_le_bytes())?;
+      writer.write_all(from.as_bytes())?;
+      writer.write_all(&(to.len() as u32).to_le_bytes())?;
+      writer.write_all(to.as_bytes())?;
+    }
+    for (media_type, data) in &self.data {
+      writer.write_all(&[serialize_media_type(*media_type)])?;
+      writer.write_all(&(data.len() as u64).to_le_bytes())?;
+      writer.write_all(data)?;
+    }
+    Ok(())
+  }
+}
+
+pub struct DenoCompileModuleData<'a> {
+  pub specifier: &'a Url,
+  pub media_type: MediaType,
+  pub data: Cow<'static, [u8]>,
+}
+
+impl<'a> DenoCompileModuleData<'a> {
+  pub fn into_for_v8(self) -> (&'a Url, ModuleType, ModuleSourceCode) {
+    fn into_bytes(data: Cow<'static, [u8]>) -> ModuleSourceCode {
+      ModuleSourceCode::Bytes(match data {
+        Cow::Borrowed(d) => d.into(),
+        Cow::Owned(d) => d.into_boxed_slice().into(),
+      })
+    }
+
+    fn into_string_unsafe(data: Cow<'static, [u8]>) -> ModuleSourceCode {
+      // todo(https://github.com/denoland/deno_core/pull/943): store whether
+      // the string is ascii or not ahead of time so we can avoid the is_ascii()
+      // check in FastString::from_static
+      match data {
+        Cow::Borrowed(d) => ModuleSourceCode::String(
+          // SAFETY: we know this is a valid utf8 string
+          unsafe { FastString::from_static(std::str::from_utf8_unchecked(d)) },
+        ),
+        Cow::Owned(d) => ModuleSourceCode::Bytes(d.into_boxed_slice().into()),
+      }
+    }
+
+    let (media_type, source) = match self.media_type {
+      MediaType::JavaScript
+      | MediaType::Jsx
+      | MediaType::Mjs
+      | MediaType::Cjs
+      | MediaType::TypeScript
+      | MediaType::Mts
+      | MediaType::Cts
+      | MediaType::Dts
+      | MediaType::Dmts
+      | MediaType::Dcts
+      | MediaType::Tsx => {
+        (ModuleType::JavaScript, into_string_unsafe(self.data))
+      }
+      MediaType::Json => (ModuleType::Json, into_string_unsafe(self.data)),
+      MediaType::Wasm => (ModuleType::Wasm, into_bytes(self.data)),
+      // just assume javascript if we made it here
+      MediaType::TsBuildInfo | MediaType::SourceMap | MediaType::Unknown => {
+        (ModuleType::JavaScript, into_bytes(self.data))
+      }
+    };
+    (self.specifier, media_type, source)
+  }
+}
+
+enum RemoteModulesStoreSpecifierValue {
+  Data(usize),
+  Redirect(Url),
+}
+
+pub struct RemoteModulesStore {
+  specifiers: HashMap<Url, RemoteModulesStoreSpecifierValue>,
+  files_data: &'static [u8],
+}
+
+impl RemoteModulesStore {
+  fn build(data: &'static [u8]) -> Result<Self, AnyError> {
+    fn read_specifier(input: &[u8]) -> Result<(&[u8], (Url, u64)), AnyError> {
+      let (input, specifier) = read_string_lossy(input)?;
+      let specifier = Url::parse(&specifier)?;
+      let (input, offset) = read_u64(input)?;
+      Ok((input, (specifier, offset)))
+    }
+
+    fn read_redirect(input: &[u8]) -> Result<(&[u8], (Url, Url)), AnyError> {
+      let (input, from) = read_string_lossy(input)?;
+      let from = Url::parse(&from)?;
+      let (input, to) = read_string_lossy(input)?;
+      let to = Url::parse(&to)?;
+      Ok((input, (from, to)))
+    }
+
+    fn read_headers(
+      input: &[u8],
+    ) -> Result<(&[u8], HashMap<Url, RemoteModulesStoreSpecifierValue>), AnyError>
+    {
+      let (input, specifiers_len) = read_u32_as_usize(input)?;
+      let (mut input, redirects_len) = read_u32_as_usize(input)?;
+      let mut specifiers =
+        HashMap::with_capacity(specifiers_len + redirects_len);
+      for _ in 0..specifiers_len {
+        let (current_input, (specifier, offset)) =
+          read_specifier(input).context("reading specifier")?;
+        input = current_input;
+        specifiers.insert(
+          specifier,
+          RemoteModulesStoreSpecifierValue::Data(offset as usize),
+        );
+      }
+
+      for _ in 0..redirects_len {
+        let (current_input, (from, to)) = read_redirect(input)?;
+        input = current_input;
+        specifiers.insert(from, RemoteModulesStoreSpecifierValue::Redirect(to));
+      }
+
+      Ok((input, specifiers))
+    }
+
+    let (files_data, specifiers) = read_headers(data)?;
+
+    Ok(Self {
+      specifiers,
+      files_data,
+    })
+  }
+
+  pub fn resolve_specifier<'a>(
+    &'a self,
+    specifier: &'a Url,
+  ) -> Result<Option<&'a Url>, AnyError> {
+    let mut count = 0;
+    let mut current = specifier;
+    loop {
+      if count > 10 {
+        bail!("Too many redirects resolving '{}'", specifier);
+      }
+      match self.specifiers.get(current) {
+        Some(RemoteModulesStoreSpecifierValue::Redirect(to)) => {
+          current = to;
+          count += 1;
+        }
+        Some(RemoteModulesStoreSpecifierValue::Data(_)) => {
+          return Ok(Some(current));
+        }
+        None => {
+          return Ok(None);
+        }
+      }
+    }
+  }
+
+  pub fn read<'a>(
+    &'a self,
+    specifier: &'a Url,
+  ) -> Result<Option<DenoCompileModuleData<'a>>, AnyError> {
+    let mut count = 0;
+    let mut current = specifier;
+    loop {
+      if count > 10 {
+        bail!("Too many redirects resolving '{}'", specifier);
+      }
+      match self.specifiers.get(current) {
+        Some(RemoteModulesStoreSpecifierValue::Redirect(to)) => {
+          current = to;
+          count += 1;
+        }
+        Some(RemoteModulesStoreSpecifierValue::Data(offset)) => {
+          let input = &self.files_data[*offset..];
+          let (input, media_type_byte) = read_bytes(input, 1)?;
+          let media_type = deserialize_media_type(media_type_byte[0])?;
+          let (input, len) = read_u64(input)?;
+          let (_input, data) = read_bytes(input, len as usize)?;
+          return Ok(Some(DenoCompileModuleData {
+            specifier,
+            media_type,
+            data: Cow::Borrowed(data),
+          }));
+        }
+        None => {
+          return Ok(None);
+        }
+      }
+    }
+  }
+}
+
+fn serialize_npm_snapshot(
+  mut snapshot: SerializedNpmResolutionSnapshot,
+) -> Vec<u8> {
+  fn append_string(bytes: &mut Vec<u8>, string: &str) {
+    let len = string.len() as u32;
+    bytes.extend_from_slice(&len.to_le_bytes());
+    bytes.extend_from_slice(string.as_bytes());
+  }
+
+  snapshot.packages.sort_by(|a, b| a.id.cmp(&b.id)); // determinism
+  let ids_to_stored_ids = snapshot
+    .packages
+    .iter()
+    .enumerate()
+    .map(|(i, pkg)| (&pkg.id, i as u32))
+    .collect::<HashMap<_, _>>();
+
+  let mut root_packages: Vec<_> = snapshot.root_packages.iter().collect();
+  root_packages.sort();
+  let mut bytes = Vec::new();
+
+  bytes.extend_from_slice(&(snapshot.packages.len() as u32).to_le_bytes());
+  for pkg in &snapshot.packages {
+    append_string(&mut bytes, &pkg.id.as_serialized());
+  }
+
+  bytes.extend_from_slice(&(root_packages.len() as u32).to_le_bytes());
+  for (req, id) in root_packages {
+    append_string(&mut bytes, &req.to_string());
+    let id = ids_to_stored_ids.get(&id).unwrap();
+    bytes.extend_from_slice(&id.to_le_bytes());
+  }
+
+  for pkg in &snapshot.packages {
+    let deps_len = pkg.dependencies.len() as u32;
+    bytes.extend_from_slice(&deps_len.to_le_bytes());
+    let mut deps: Vec<_> = pkg.dependencies.iter().collect();
+    deps.sort();
+    for (req, id) in deps {
+      append_string(&mut bytes, req);
+      let id = ids_to_stored_ids.get(&id).unwrap();
+      bytes.extend_from_slice(&id.to_le_bytes());
+    }
+  }
+
+  bytes
+}
+
+fn deserialize_npm_snapshot(
+  input: &[u8],
+) -> Result<ValidSerializedNpmResolutionSnapshot, AnyError> {
+  fn parse_id(input: &[u8]) -> Result<(&[u8], NpmPackageId), AnyError> {
+    let (input, id) = read_string_lossy(input)?;
+    let id = NpmPackageId::from_serialized(&id)?;
+    Ok((input, id))
+  }
+
+  #[allow(clippy::needless_lifetimes)] // clippy bug
+  fn parse_root_package<'a>(
+    id_to_npm_id: &'a impl Fn(usize) -> Result<NpmPackageId, AnyError>,
+  ) -> impl Fn(&[u8]) -> Result<(&[u8], (PackageReq, NpmPackageId)), AnyError> + 'a
+  {
+    |input| {
+      let (input, req) = read_string_lossy(input)?;
+      let req = PackageReq::from_str(&req)?;
+      let (input, id) = read_u32_as_usize(input)?;
+      Ok((input, (req, id_to_npm_id(id)?)))
+    }
+  }
+
+  #[allow(clippy::needless_lifetimes)] // clippy bug
+  fn parse_package_dep<'a>(
+    id_to_npm_id: &'a impl Fn(usize) -> Result<NpmPackageId, AnyError>,
+  ) -> impl Fn(&[u8]) -> Result<(&[u8], (String, NpmPackageId)), AnyError> + 'a
+  {
+    |input| {
+      let (input, req) = read_string_lossy(input)?;
+      let (input, id) = read_u32_as_usize(input)?;
+      Ok((input, (req.into_owned(), id_to_npm_id(id)?)))
+    }
+  }
+
+  fn parse_package<'a>(
+    input: &'a [u8],
+    id: NpmPackageId,
+    id_to_npm_id: &impl Fn(usize) -> Result<NpmPackageId, AnyError>,
+  ) -> Result<(&'a [u8], SerializedNpmResolutionSnapshotPackage), AnyError> {
+    let (input, deps_len) = read_u32_as_usize(input)?;
+    let (input, dependencies) =
+      parse_hashmap_n_times(input, deps_len, parse_package_dep(id_to_npm_id))?;
+    Ok((
+      input,
+      SerializedNpmResolutionSnapshotPackage {
+        id,
+        system: Default::default(),
+        dist: Default::default(),
+        dependencies,
+        optional_dependencies: Default::default(),
+        bin: None,
+        scripts: Default::default(),
+        deprecated: Default::default(),
+      },
+    ))
+  }
+
+  let (input, packages_len) = read_u32_as_usize(input)?;
+
+  // get a hashmap of all the npm package ids to their serialized ids
+  let (input, data_ids_to_npm_ids) =
+    parse_vec_n_times(input, packages_len, parse_id)
+      .context("deserializing id")?;
+  let data_id_to_npm_id = |id: usize| {
+    data_ids_to_npm_ids
+      .get(id)
+      .cloned()
+      .ok_or_else(|| deno_core::anyhow::anyhow!("Invalid npm package id"))
+  };
+
+  let (input, root_packages_len) = read_u32_as_usize(input)?;
+  let (input, root_packages) = parse_hashmap_n_times(
+    input,
+    root_packages_len,
+    parse_root_package(&data_id_to_npm_id),
+  )
+  .context("deserializing root package")?;
+  let (input, packages) =
+    parse_vec_n_times_with_index(input, packages_len, |input, index| {
+      parse_package(input, data_id_to_npm_id(index)?, &data_id_to_npm_id)
+    })
+    .context("deserializing package")?;
+
+  if !input.is_empty() {
+    bail!("Unexpected data left over");
+  }
+
+  Ok(
+    SerializedNpmResolutionSnapshot {
+      packages,
+      root_packages,
+    }
+    // this is ok because we have already verified that all the
+    // identifiers found in the snapshot are valid via the
+    // npm package id -> npm package id mapping
+    .into_valid_unsafe(),
+  )
+}
+
+fn serialize_media_type(media_type: MediaType) -> u8 {
+  match media_type {
+    MediaType::JavaScript => 0,
+    MediaType::Jsx => 1,
+    MediaType::Mjs => 2,
+    MediaType::Cjs => 3,
+    MediaType::TypeScript => 4,
+    MediaType::Mts => 5,
+    MediaType::Cts => 6,
+    MediaType::Dts => 7,
+    MediaType::Dmts => 8,
+    MediaType::Dcts => 9,
+    MediaType::Tsx => 10,
+    MediaType::Json => 11,
+    MediaType::Wasm => 12,
+    MediaType::TsBuildInfo => 13,
+    MediaType::SourceMap => 14,
+    MediaType::Unknown => 15,
+  }
+}
+
+fn deserialize_media_type(value: u8) -> Result<MediaType, AnyError> {
+  match value {
+    0 => Ok(MediaType::JavaScript),
+    1 => Ok(MediaType::Jsx),
+    2 => Ok(MediaType::Mjs),
+    3 => Ok(MediaType::Cjs),
+    4 => Ok(MediaType::TypeScript),
+    5 => Ok(MediaType::Mts),
+    6 => Ok(MediaType::Cts),
+    7 => Ok(MediaType::Dts),
+    8 => Ok(MediaType::Dmts),
+    9 => Ok(MediaType::Dcts),
+    10 => Ok(MediaType::Tsx),
+    11 => Ok(MediaType::Json),
+    12 => Ok(MediaType::Wasm),
+    13 => Ok(MediaType::TsBuildInfo),
+    14 => Ok(MediaType::SourceMap),
+    15 => Ok(MediaType::Unknown),
+    _ => bail!("Unknown media type value: {}", value),
+  }
+}
+
+fn parse_hashmap_n_times<TKey: std::cmp::Eq + std::hash::Hash, TValue>(
+  mut input: &[u8],
+  times: usize,
+  parse: impl Fn(&[u8]) -> Result<(&[u8], (TKey, TValue)), AnyError>,
+) -> Result<(&[u8], HashMap<TKey, TValue>), AnyError> {
+  let mut results = HashMap::with_capacity(times);
+  for _ in 0..times {
+    let result = parse(input);
+    let (new_input, (key, value)) = result?;
+    results.insert(key, value);
+    input = new_input;
+  }
+  Ok((input, results))
+}
+
+fn parse_vec_n_times<TResult>(
+  input: &[u8],
+  times: usize,
+  parse: impl Fn(&[u8]) -> Result<(&[u8], TResult), AnyError>,
+) -> Result<(&[u8], Vec<TResult>), AnyError> {
+  parse_vec_n_times_with_index(input, times, |input, _index| parse(input))
+}
+
+fn parse_vec_n_times_with_index<TResult>(
+  mut input: &[u8],
+  times: usize,
+  parse: impl Fn(&[u8], usize) -> Result<(&[u8], TResult), AnyError>,
+) -> Result<(&[u8], Vec<TResult>), AnyError> {
+  let mut results = Vec::with_capacity(times);
+  for i in 0..times {
+    let result = parse(input, i);
+    let (new_input, result) = result?;
+    results.push(result);
+    input = new_input;
+  }
+  Ok((input, results))
+}
+
+fn read_bytes(input: &[u8], len: usize) -> Result<(&[u8], &[u8]), AnyError> {
+  if input.len() < len {
+    bail!("Unexpected end of data.",);
+  }
+  let (len_bytes, input) = input.split_at(len);
+  Ok((input, len_bytes))
+}
+
+fn read_string_lossy(input: &[u8]) -> Result<(&[u8], Cow<str>), AnyError> {
+  let (input, str_len) = read_u32_as_usize(input)?;
+  let (input, data_bytes) = read_bytes(input, str_len)?;
+  Ok((input, String::from_utf8_lossy(data_bytes)))
+}
+
+fn read_u32_as_usize(input: &[u8]) -> Result<(&[u8], usize), AnyError> {
+  let (input, len_bytes) = read_bytes(input, 4)?;
+  let len = u32::from_le_bytes(len_bytes.try_into()?);
+  Ok((input, len as usize))
+}
+
+fn read_u64(input: &[u8]) -> Result<(&[u8], u64), AnyError> {
+  let (input, len_bytes) = read_bytes(input, 8)?;
+  let len = u64::from_le_bytes(len_bytes.try_into()?);
+  Ok((input, len))
+}
diff --git a/cli/standalone/virtual_fs.rs b/cli/standalone/virtual_fs.rs
index 53d045b625..0ae00accbf 100644
--- a/cli/standalone/virtual_fs.rs
+++ b/cli/standalone/virtual_fs.rs
@@ -7,6 +7,7 @@ use std::fs::File;
 use std::io::Read;
 use std::io::Seek;
 use std::io::SeekFrom;
+use std::ops::Range;
 use std::path::Path;
 use std::path::PathBuf;
 use std::rc::Rc;
@@ -67,6 +68,26 @@ impl VfsBuilder {
     })
   }
 
+  pub fn set_new_root_path(
+    &mut self,
+    root_path: PathBuf,
+  ) -> Result<(), AnyError> {
+    let root_path = canonicalize_path(&root_path)?;
+    self.root_path = root_path;
+    self.root_dir = VirtualDirectory {
+      name: self
+        .root_path
+        .file_stem()
+        .map(|s| s.to_string_lossy().into_owned())
+        .unwrap_or("root".to_string()),
+      entries: vec![VfsEntry::Dir(VirtualDirectory {
+        name: std::mem::take(&mut self.root_dir.name),
+        entries: std::mem::take(&mut self.root_dir.entries),
+      })],
+    };
+    Ok(())
+  }
+
   pub fn with_root_dir<R>(
     &mut self,
     with_root: impl FnOnce(&mut VirtualDirectory) -> R,
@@ -119,7 +140,7 @@ impl VfsBuilder {
                 // inline the symlink and make the target file
                 let file_bytes = std::fs::read(&target)
                   .with_context(|| format!("Reading {}", path.display()))?;
-                self.add_file(&path, file_bytes)?;
+                self.add_file_with_data_inner(&path, file_bytes)?;
               } else {
                 log::warn!(
                   "{} Symlink target is outside '{}'. Excluding symlink at '{}' with target '{}'.",
@@ -191,16 +212,32 @@ impl VfsBuilder {
     self.add_file_at_path_not_symlink(&target_path)
   }
 
-  pub fn add_file_at_path_not_symlink(
+  fn add_file_at_path_not_symlink(
     &mut self,
     path: &Path,
   ) -> Result<(), AnyError> {
     let file_bytes = std::fs::read(path)
       .with_context(|| format!("Reading {}", path.display()))?;
-    self.add_file(path, file_bytes)
+    self.add_file_with_data_inner(path, file_bytes)
   }
 
-  fn add_file(&mut self, path: &Path, data: Vec<u8>) -> Result<(), AnyError> {
+  pub fn add_file_with_data(
+    &mut self,
+    path: &Path,
+    data: Vec<u8>,
+  ) -> Result<(), AnyError> {
+    let target_path = canonicalize_path(path)?;
+    if target_path != path {
+      self.add_symlink(path, &target_path)?;
+    }
+    self.add_file_with_data_inner(&target_path, data)
+  }
+
+  fn add_file_with_data_inner(
+    &mut self,
+    path: &Path,
+    data: Vec<u8>,
+  ) -> Result<(), AnyError> {
     log::debug!("Adding file '{}'", path.display());
     let checksum = util::checksum::gen(&[&data]);
     let offset = if let Some(offset) = self.file_offsets.get(&checksum) {
@@ -249,8 +286,15 @@ impl VfsBuilder {
       path.display(),
       target.display()
     );
-    let dest = self.path_relative_root(target)?;
-    if dest == self.path_relative_root(path)? {
+    let relative_target = self.path_relative_root(target)?;
+    let relative_path = match self.path_relative_root(path) {
+      Ok(path) => path,
+      Err(StripRootError { .. }) => {
+        // ignore if the original path is outside the root directory
+        return Ok(());
+      }
+    };
+    if relative_target == relative_path {
       // it's the same, ignore
       return Ok(());
     }
@@ -263,7 +307,7 @@ impl VfsBuilder {
           insert_index,
           VfsEntry::Symlink(VirtualSymlink {
             name: name.to_string(),
-            dest_parts: dest
+            dest_parts: relative_target
               .components()
               .map(|c| c.as_os_str().to_string_lossy().to_string())
               .collect::<Vec<_>>(),
@@ -751,14 +795,14 @@ impl deno_io::fs::File for FileBackedVfsFile {
 
 #[derive(Debug)]
 pub struct FileBackedVfs {
-  file: Mutex<Vec<u8>>,
+  vfs_data: Cow<'static, [u8]>,
   fs_root: VfsRoot,
 }
 
 impl FileBackedVfs {
-  pub fn new(file: Vec<u8>, fs_root: VfsRoot) -> Self {
+  pub fn new(data: Cow<'static, [u8]>, fs_root: VfsRoot) -> Self {
     Self {
-      file: Mutex::new(file),
+      vfs_data: data,
       fs_root,
     }
   }
@@ -827,10 +871,15 @@ impl FileBackedVfs {
     Ok(path)
   }
 
-  pub fn read_file_all(&self, file: &VirtualFile) -> std::io::Result<Vec<u8>> {
-    let mut buf = vec![0; file.len as usize];
-    self.read_file(file, 0, &mut buf)?;
-    Ok(buf)
+  pub fn read_file_all(
+    &self,
+    file: &VirtualFile,
+  ) -> std::io::Result<Cow<'static, [u8]>> {
+    let read_range = self.get_read_range(file, 0, file.len)?;
+    match &self.vfs_data {
+      Cow::Borrowed(data) => Ok(Cow::Borrowed(&data[read_range])),
+      Cow::Owned(data) => Ok(Cow::Owned(data[read_range].to_vec())),
+    }
   }
 
   pub fn read_file(
@@ -839,18 +888,27 @@ impl FileBackedVfs {
     pos: u64,
     buf: &mut [u8],
   ) -> std::io::Result<usize> {
-    let data = self.file.lock();
+    let read_range = self.get_read_range(file, pos, buf.len() as u64)?;
+    buf.copy_from_slice(&self.vfs_data[read_range]);
+    Ok(buf.len())
+  }
+
+  fn get_read_range(
+    &self,
+    file: &VirtualFile,
+    pos: u64,
+    len: u64,
+  ) -> std::io::Result<Range<usize>> {
+    let data = &self.vfs_data;
     let start = self.fs_root.start_file_offset + file.offset + pos;
-    let end = start + buf.len() as u64;
+    let end = start + len;
     if end > data.len() as u64 {
       return Err(std::io::Error::new(
         std::io::ErrorKind::UnexpectedEof,
         "unexpected EOF",
       ));
     }
-
-    buf.copy_from_slice(&data[start as usize..end as usize]);
-    Ok(buf.len())
+    Ok(start as usize..end as usize)
   }
 
   pub fn dir_entry(&self, path: &Path) -> std::io::Result<&VirtualDirectory> {
@@ -888,7 +946,7 @@ mod test {
   #[track_caller]
   fn read_file(vfs: &FileBackedVfs, path: &Path) -> String {
     let file = vfs.file_entry(path).unwrap();
-    String::from_utf8(vfs.read_file_all(file).unwrap()).unwrap()
+    String::from_utf8(vfs.read_file_all(file).unwrap().into_owned()).unwrap()
   }
 
   #[test]
@@ -901,20 +959,23 @@ mod test {
     let src_path = src_path.to_path_buf();
     let mut builder = VfsBuilder::new(src_path.clone()).unwrap();
     builder
-      .add_file(&src_path.join("a.txt"), "data".into())
+      .add_file_with_data_inner(&src_path.join("a.txt"), "data".into())
       .unwrap();
     builder
-      .add_file(&src_path.join("b.txt"), "data".into())
+      .add_file_with_data_inner(&src_path.join("b.txt"), "data".into())
       .unwrap();
     assert_eq!(builder.files.len(), 1); // because duplicate data
     builder
-      .add_file(&src_path.join("c.txt"), "c".into())
+      .add_file_with_data_inner(&src_path.join("c.txt"), "c".into())
       .unwrap();
     builder
-      .add_file(&src_path.join("sub_dir").join("d.txt"), "d".into())
+      .add_file_with_data_inner(
+        &src_path.join("sub_dir").join("d.txt"),
+        "d".into(),
+      )
       .unwrap();
     builder
-      .add_file(&src_path.join("e.txt"), "e".into())
+      .add_file_with_data_inner(&src_path.join("e.txt"), "e".into())
       .unwrap();
     builder
       .add_symlink(
@@ -1031,7 +1092,7 @@ mod test {
     (
       dest_path.to_path_buf(),
       FileBackedVfs::new(
-        data,
+        Cow::Owned(data),
         VfsRoot {
           dir: root_dir,
           root_path: dest_path.to_path_buf(),
@@ -1082,7 +1143,7 @@ mod test {
     let temp_path = temp_dir.path().canonicalize();
     let mut builder = VfsBuilder::new(temp_path.to_path_buf()).unwrap();
     builder
-      .add_file(
+      .add_file_with_data_inner(
         temp_path.join("a.txt").as_path(),
         "0123456789".to_string().into_bytes(),
       )
diff --git a/cli/tools/compile.rs b/cli/tools/compile.rs
index 3cc4414fcb..5a4a938bb9 100644
--- a/cli/tools/compile.rs
+++ b/cli/tools/compile.rs
@@ -5,6 +5,7 @@ use crate::args::CompileFlags;
 use crate::args::Flags;
 use crate::factory::CliFactory;
 use crate::http_util::HttpClientProvider;
+use crate::standalone::binary::StandaloneRelativeFileBaseUrl;
 use crate::standalone::is_standalone_binary;
 use deno_ast::ModuleSpecifier;
 use deno_core::anyhow::bail;
@@ -14,7 +15,6 @@ use deno_core::error::AnyError;
 use deno_core::resolve_url_or_path;
 use deno_graph::GraphKind;
 use deno_terminal::colors;
-use eszip::EszipRelativeFileBaseUrl;
 use rand::Rng;
 use std::path::Path;
 use std::path::PathBuf;
@@ -29,7 +29,6 @@ pub async fn compile(
   let factory = CliFactory::from_flags(flags);
   let cli_options = factory.cli_options()?;
   let module_graph_creator = factory.module_graph_creator().await?;
-  let parsed_source_cache = factory.parsed_source_cache();
   let binary_writer = factory.create_compile_binary_writer().await?;
   let http_client = factory.http_client_provider();
   let module_specifier = cli_options.resolve_main_module()?;
@@ -80,7 +79,7 @@ pub async fn compile(
   let graph = if cli_options.type_check_mode().is_true() {
     // In this case, the previous graph creation did type checking, which will
     // create a module graph with types information in it. We don't want to
-    // store that in the eszip so create a code only module graph from scratch.
+    // store that in the binary so create a code only module graph from scratch.
     module_graph_creator
       .create_graph(GraphKind::CodeOnly, module_roots)
       .await?
@@ -91,11 +90,6 @@ pub async fn compile(
   let ts_config_for_emit = cli_options
     .resolve_ts_config_for_emit(deno_config::deno_json::TsConfigType::Emit)?;
   check_warn_tsconfig(&ts_config_for_emit);
-  let (transpile_options, emit_options) =
-    crate::args::ts_config_to_transpile_and_emit_options(
-      ts_config_for_emit.ts_config,
-    )?;
-  let parser = parsed_source_cache.as_capturing_parser();
   let root_dir_url = resolve_root_dir_from_specifiers(
     cli_options.workspace().root_dir(),
     graph.specifiers().map(|(s, _)| s).chain(
@@ -106,17 +100,6 @@ pub async fn compile(
     ),
   );
   log::debug!("Binary root dir: {}", root_dir_url);
-  let root_dir_url = EszipRelativeFileBaseUrl::new(&root_dir_url);
-  let eszip = eszip::EszipV2::from_graph(eszip::FromGraphOptions {
-    graph,
-    parser,
-    transpile_options,
-    emit_options,
-    // make all the modules relative to the root folder
-    relative_file_base: Some(root_dir_url),
-    npm_packages: None,
-  })?;
-
   log::info!(
     "{} {} to {}",
     colors::green("Compile"),
@@ -143,15 +126,18 @@ pub async fn compile(
   let write_result = binary_writer
     .write_bin(
       file,
-      eszip,
-      root_dir_url,
+      &graph,
+      StandaloneRelativeFileBaseUrl::from(&root_dir_url),
       module_specifier,
       &compile_flags,
       cli_options,
     )
     .await
     .with_context(|| {
-      format!("Writing temporary file '{}'", temp_path.display())
+      format!(
+        "Writing deno compile executable to temporary file '{}'",
+        temp_path.display()
+      )
     });
 
   // set it as executable
diff --git a/cli/util/text_encoding.rs b/cli/util/text_encoding.rs
index 0b7601cb9c..df72cc2be6 100644
--- a/cli/util/text_encoding.rs
+++ b/cli/util/text_encoding.rs
@@ -103,6 +103,21 @@ pub fn arc_str_to_bytes(arc_str: Arc<str>) -> Arc<[u8]> {
   unsafe { Arc::from_raw(raw as *const [u8]) }
 }
 
+/// Converts an `Arc<u8>` to an `Arc<str>` if able.
+#[allow(dead_code)]
+pub fn arc_u8_to_arc_str(
+  arc_u8: Arc<[u8]>,
+) -> Result<Arc<str>, std::str::Utf8Error> {
+  // Check that the string is valid UTF-8.
+  std::str::from_utf8(&arc_u8)?;
+  // SAFETY: the string is valid UTF-8, and the layout Arc<[u8]> is the same as
+  // Arc<str>. This is proven by the From<Arc<str>> impl for Arc<[u8]> from the
+  // standard library.
+  Ok(unsafe {
+    std::mem::transmute::<std::sync::Arc<[u8]>, std::sync::Arc<str>>(arc_u8)
+  })
+}
+
 #[cfg(test)]
 mod tests {
   use std::sync::Arc;
diff --git a/tests/specs/compile/byonm_main_sub_dir/deno.json b/tests/specs/compile/byonm_main_sub_dir/deno.json
index 6134d86d1c..fde86a1efb 100644
--- a/tests/specs/compile/byonm_main_sub_dir/deno.json
+++ b/tests/specs/compile/byonm_main_sub_dir/deno.json
@@ -1,3 +1,3 @@
 {
-  "unstable": ["byonm"]
+  "nodeModulesDir": "manual"
 }
diff --git a/tests/specs/compile/detect_cjs/output.out b/tests/specs/compile/detect_cjs/output.out
index b53c443698..e1c27b8dcf 100644
--- a/tests/specs/compile/detect_cjs/output.out
+++ b/tests/specs/compile/detect_cjs/output.out
@@ -1 +1,2 @@
-error: Module not found: file:///[WILDLINE]/add.js
+error: Uncaught SyntaxError: The requested module './add.js' does not provide an export named 'add'
+    at <anonymous> (file:///[WILDLINE])