diff --git a/cli/flags.rs b/cli/flags.rs
index 6d6129c7a8..f2a3ffc368 100644
--- a/cli/flags.rs
+++ b/cli/flags.rs
@@ -485,7 +485,6 @@ fn run_test_args_parse(flags: &mut DenoFlags, matches: &clap::ArgMatches) {
 fn run_parse(flags: &mut DenoFlags, matches: &clap::ArgMatches) {
   flags.subcommand = DenoSubcommand::Run;
   script_arg_parse(flags, matches);
-  args_parse(flags, matches);
   run_test_args_parse(flags, matches);
 }
 
@@ -925,7 +924,6 @@ fn run_subcommand<'a, 'b>() -> App<'a, 'b> {
   run_test_args(SubCommand::with_name("run"))
     .setting(AppSettings::TrailingVarArg)
     .arg(script_arg())
-    .arg(args_arg())
     .about("Run a program given a filename or url to the source code")
     .long_about(
       "Run a program given a filename or url to the source code.
@@ -945,11 +943,7 @@ With only permission to read from disk and listen to network
 
 With only permission to read whitelist files from disk
 
-  deno run --allow-read=/etc https://deno.land/std/http/file_server.ts
-
-Any arguments that should be passed to the script should be prefixed by '--'
-
-  deno run -A https://deno.land/std/examples/cat.ts -- /etc/passwd",
+  deno run --allow-read=/etc https://deno.land/std/http/file_server.ts",
     )
 }
 
@@ -994,26 +988,15 @@ _test.js and executes them.
 }
 
 fn script_arg<'a, 'b>() -> Arg<'a, 'b> {
-  Arg::with_name("script").help("script").value_name("SCRIPT")
+  Arg::with_name("script_arg")
+    .multiple(true)
+    .help("script args")
+    .value_name("SCRIPT_ARG")
 }
 
 fn script_arg_parse(flags: &mut DenoFlags, matches: &ArgMatches) {
-  if let Some(script_value) = matches.value_of("script") {
-    debug_assert!(flags.argv.len() == 1);
-    flags.argv.push(String::from(script_value));
-  }
-}
-
-fn args_arg<'a, 'b>() -> Arg<'a, 'b> {
-  Arg::with_name("script_args")
-    .raw(true)
-    .help("script args")
-    .value_name("SCRIPT_ARGS")
-}
-
-fn args_parse(flags: &mut DenoFlags, matches: &ArgMatches) {
-  if let Some(values) = matches.values_of("script_args") {
-    for v in values {
+  if let Some(script_values) = matches.values_of("script_arg") {
+    for v in script_values {
       flags.argv.push(String::from(v));
     }
   }
@@ -1341,7 +1324,6 @@ mod tests {
       "run",
       "--allow-net",
       "gist.ts",
-      "--",
       "--title",
       "X"
     ]);
@@ -1424,7 +1406,7 @@ mod tests {
       r.unwrap(),
       DenoFlags {
         subcommand: DenoSubcommand::Run,
-        argv: svec!["deno", "script.ts", "-D", "--allow-net"],
+        argv: svec!["deno", "script.ts", "--", "-D", "--allow-net"],
         allow_write: true,
         ..DenoFlags::default()
       }
diff --git a/cli/tests/integration_tests.rs b/cli/tests/integration_tests.rs
index 91c30a51d7..eea1dd2c98 100644
--- a/cli/tests/integration_tests.rs
+++ b/cli/tests/integration_tests.rs
@@ -253,7 +253,7 @@ itest!(_027_redirect_typescript {
 });
 
 itest!(_028_args {
-  args: "run --reload 028_args.ts -- --arg1 val1 --arg2=val2 -- arg3 arg4",
+  args: "run --reload 028_args.ts --arg1 val1 --arg2=val2 -- arg3 arg4",
   output: "028_args.ts.out",
 });
 
diff --git a/cli/tests/std_tests.rs b/cli/tests/std_tests.rs
index 8ad971d7c0..7b7928f70b 100644
--- a/cli/tests/std_tests.rs
+++ b/cli/tests/std_tests.rs
@@ -23,7 +23,6 @@ mod tests {
       .arg("-A")
       // .arg("-Ldebug")
       .arg("./testing/runner.ts")
-      .arg("--")
       .arg("--exclude=testing/testdata")
       .spawn()
       .expect("failed to spawn script");
diff --git a/std/examples/test.ts b/std/examples/test.ts
index 646eb5d336..26dd989e47 100644
--- a/std/examples/test.ts
+++ b/std/examples/test.ts
@@ -20,7 +20,6 @@ test(async function catSmoke(): Promise<void> {
       "run",
       "--allow-read",
       "examples/cat.ts",
-      "--",
       "README.md"
     ],
     stdout: "piped"
diff --git a/std/fs/empty_dir_test.ts b/std/fs/empty_dir_test.ts
index 1c1e6f34df..55fdb52dc0 100644
--- a/std/fs/empty_dir_test.ts
+++ b/std/fs/empty_dir_test.ts
@@ -217,13 +217,12 @@ test(async function emptyDirPermission(): Promise<void> {
       args.push(
         path.join(testdataDir, s.async ? "empty_dir.ts" : "empty_dir_sync.ts")
       );
-      args.push("--");
       args.push("testfolder");
 
       const { stdout } = Deno.run({
         stdout: "piped",
         cwd: testdataDir,
-        args
+        args: args
       });
 
       const output = await Deno.readAll(stdout);
diff --git a/std/fs/exists_test.ts b/std/fs/exists_test.ts
index 8e9381ed2e..b8c968a028 100644
--- a/std/fs/exists_test.ts
+++ b/std/fs/exists_test.ts
@@ -124,7 +124,6 @@ test(async function existsPermission(): Promise<void> {
     }
 
     args.push(path.join(testdataDir, s.async ? "exists.ts" : "exists_sync.ts"));
-    args.push("--");
     args.push(s.file);
 
     const { stdout } = Deno.run({
diff --git a/std/http/file_server_test.ts b/std/http/file_server_test.ts
index e710b620ce..170979b614 100644
--- a/std/http/file_server_test.ts
+++ b/std/http/file_server_test.ts
@@ -14,7 +14,6 @@ async function startFileServer(): Promise<void> {
       "--allow-read",
       "--allow-net",
       "http/file_server.ts",
-      "--",
       ".",
       "--cors"
     ],
@@ -123,7 +122,7 @@ test(async function servePermissionDenied(): Promise<void> {
 
 test(async function printHelp(): Promise<void> {
   const helpProcess = Deno.run({
-    args: [Deno.execPath(), "run", "http/file_server.ts", "--", "--help"],
+    args: [Deno.execPath(), "run", "http/file_server.ts", "--help"],
     stdout: "piped"
   });
   const r = new TextProtoReader(new BufReader(helpProcess.stdout!));
diff --git a/std/installer/mod.ts b/std/installer/mod.ts
index 1d9558520d..ce6c40f37c 100644
--- a/std/installer/mod.ts
+++ b/std/installer/mod.ts
@@ -255,7 +255,6 @@ export async function install(
     "run",
     ...grantedPermissions.map(getFlagFromPermission),
     moduleUrl,
-    "--",
     ...scriptArgs
   ];
 
diff --git a/std/installer/test.ts b/std/installer/test.ts
index bafe607cc1..5239dc157c 100644
--- a/std/installer/test.ts
+++ b/std/installer/test.ts
@@ -1,5 +1,5 @@
 // Copyright 2018-2020 the Deno authors. All rights reserved. MIT license.
-const { run, stat, makeTempDir, remove, env } = Deno;
+const { run, stat, makeTempDir, remove, env, readAll } = Deno;
 
 import { test, runIfMain, TestFunction } from "../testing/mod.ts";
 import { assert, assertEquals } from "../testing/asserts.ts";
@@ -20,7 +20,6 @@ async function startFileServer(): Promise<void> {
       "--allow-read",
       "--allow-net",
       "http/file_server.ts",
-      "--",
       ".",
       "--cors"
     ],
@@ -84,11 +83,11 @@ installerTest(async function installBasic(): Promise<void> {
       /* eslint-disable max-len */
       `% This executable is generated by Deno. Please don't modify it unless you know what it means. %
 @IF EXIST "%~dp0\deno.exe" (
-  "%~dp0\deno.exe" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" %*
+  "%~dp0\deno.exe" "run" "http://localhost:4500/installer/testdata/echo.ts" %*
 ) ELSE (
   @SETLOCAL
   @SET PATHEXT=%PATHEXT:;.TS;=;%
-  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" %*
+  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" %*
 )
 `
       /* eslint-enable max-len */
@@ -107,10 +106,10 @@ case \`uname\` in
 esac
 
 if [ -x "$basedir/deno" ]; then
-  "$basedir/deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" "$@"
+  "$basedir/deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "$@"
   ret=$?
 else
-  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" "$@"
+  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "$@"
   ret=$?
 fi
 exit $ret
@@ -139,11 +138,11 @@ installerTest(async function installCustomDir(): Promise<void> {
       /* eslint-disable max-len */
       `% This executable is generated by Deno. Please don't modify it unless you know what it means. %
 @IF EXIST "%~dp0\deno.exe" (
-  "%~dp0\deno.exe" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" %*
+  "%~dp0\deno.exe" "run" "http://localhost:4500/installer/testdata/echo.ts" %*
 ) ELSE (
   @SETLOCAL
   @SET PATHEXT=%PATHEXT:;.TS;=;%
-  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" %*
+  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" %*
 )
 `
       /* eslint-enable max-len */
@@ -162,10 +161,10 @@ case \`uname\` in
 esac
 
 if [ -x "$basedir/deno" ]; then
-  "$basedir/deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" "$@"
+  "$basedir/deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "$@"
   ret=$?
 else
-  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" "$@"
+  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "$@"
   ret=$?
 fi
 exit $ret
@@ -193,11 +192,11 @@ installerTest(async function installLocalModule(): Promise<void> {
       /* eslint-disable max-len */
       `% This executable is generated by Deno. Please don't modify it unless you know what it means. %
 @IF EXIST "%~dp0\deno.exe" (
-  "%~dp0\deno.exe" "run" "${localModule}" "--" %*
+  "%~dp0\deno.exe" "run" "${localModule}" %*
 ) ELSE (
   @SETLOCAL
   @SET PATHEXT=%PATHEXT:;.TS;=;%
-  "deno" "run" "${localModule}" "--" %*
+  "deno" "run" "${localModule}" %*
 )
 `
       /* eslint-enable max-len */
@@ -216,10 +215,10 @@ case \`uname\` in
 esac
 
 if [ -x "$basedir/deno" ]; then
-  "$basedir/deno" "run" "${localModule}" "--" "$@"
+  "$basedir/deno" "run" "${localModule}" "$@"
   ret=$?
 else
-  "deno" "run" "${localModule}" "--" "$@"
+  "deno" "run" "${localModule}" "$@"
   ret=$?
 fi
 exit $ret
@@ -228,17 +227,57 @@ exit $ret
   );
 });
 
-/* TODO(ry) Re-enable this test
 installerTest(async function installWithFlags(): Promise<void> {
   await install(
     "echo_test",
     "http://localhost:4500/installer/testdata/echo.ts",
     ["--allow-net", "--allow-read", "--foobar"]
   );
-});
-*/
 
-/* TODO(ry) Re-enable this test
+  const { HOME } = env();
+  const filePath = path.resolve(HOME, ".deno/bin/echo_test");
+
+  if (path.isWindows) {
+    assertEquals(
+      await fs.readFileStr(filePath + ".cmd"),
+      /* eslint-disable max-len */
+      `% This executable is generated by Deno. Please don't modify it unless you know what it means. %
+@IF EXIST "%~dp0\deno.exe" (
+  "%~dp0\deno.exe" "run" "--allow-net" "--allow-read" "http://localhost:4500/installer/testdata/echo.ts" "--foobar" %*
+) ELSE (
+  @SETLOCAL
+  @SET PATHEXT=%PATHEXT:;.TS;=;%
+  "deno" "run" "--allow-net" "--allow-read" "http://localhost:4500/installer/testdata/echo.ts" "--foobar" %*
+)
+`
+      /* eslint-enable max-len */
+    );
+  }
+
+  assertEquals(
+    await fs.readFileStr(filePath),
+    /* eslint-disable max-len */
+    `#!/bin/sh
+# This executable is generated by Deno. Please don't modify it unless you know what it means.
+basedir=$(dirname "$(echo "$0" | sed -e 's,\\\\,/,g')")
+
+case \`uname\` in
+  *CYGWIN*) basedir=\`cygpath -w "$basedir"\`;;
+esac
+
+if [ -x "$basedir/deno" ]; then
+  "$basedir/deno" "run" "--allow-net" "--allow-read" "http://localhost:4500/installer/testdata/echo.ts" "--foobar" "$@"
+  ret=$?
+else
+  "deno" "run" "--allow-net" "--allow-read" "http://localhost:4500/installer/testdata/echo.ts" "--foobar" "$@"
+  ret=$?
+fi
+exit $ret
+`
+    /* eslint-enable max-len */
+  );
+});
+
 installerTest(async function installLocalModuleAndRun(): Promise<void> {
   const tempDir = await makeTempDir();
   const localModule = path.join(Deno.cwd(), "installer", "testdata", "echo.ts");
@@ -276,9 +315,7 @@ installerTest(async function installLocalModuleAndRun(): Promise<void> {
 
   assert(!thrown, "It should not throw an error");
 }, true); // set true to install module in your real $HOME dir.
-*/
 
-/* TODO(ry) Re-enable this test
 installerTest(async function installAndMakesureItCanRun(): Promise<void> {
   const tempDir = await makeTempDir();
   await install(
@@ -320,9 +357,7 @@ installerTest(async function installAndMakesureItCanRun(): Promise<void> {
 
   assert(!thrown, "It should not throw an error");
 }, true); // set true to install module in your real $HOME dir.
-*/
 
-/* TODO(ry) Re-enable this test
 installerTest(async function installAndMakesureArgsRight(): Promise<void> {
   const tempDir = await makeTempDir();
   await install(
@@ -350,7 +385,9 @@ installerTest(async function installAndMakesureArgsRight(): Promise<void> {
 
   try {
     const b = await readAll(ps.stdout);
+
     const s = new TextDecoder("utf-8").decode(b);
+
     const obj = JSON.parse(s);
 
     assertEquals(obj[0], "arg1");
@@ -367,7 +404,6 @@ installerTest(async function installAndMakesureArgsRight(): Promise<void> {
 
   assert(!thrown, "It should not throw an error");
 }, true); // set true to install module in your real $HOME dir.
- */
 
 installerTest(async function installWithoutHOMEVar(): Promise<void> {
   const { HOME } = env();
@@ -391,11 +427,11 @@ installerTest(async function installWithoutHOMEVar(): Promise<void> {
       /* eslint-disable max-len */
       `% This executable is generated by Deno. Please don't modify it unless you know what it means. %
 @IF EXIST "%~dp0\deno.exe" (
-  "%~dp0\deno.exe" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" %*
+  "%~dp0\deno.exe" "run" "http://localhost:4500/installer/testdata/echo.ts" %*
 ) ELSE (
   @SETLOCAL
   @SET PATHEXT=%PATHEXT:;.TS;=;%
-  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" %*
+  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" %*
 )
 `
       /* eslint-enable max-len */
@@ -414,10 +450,10 @@ case \`uname\` in
 esac
 
 if [ -x "$basedir/deno" ]; then
-  "$basedir/deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" "$@"
+  "$basedir/deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "$@"
   ret=$?
 else
-  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "--" "$@"
+  "deno" "run" "http://localhost:4500/installer/testdata/echo.ts" "$@"
   ret=$?
 fi
 exit $ret
diff --git a/std/manual.md b/std/manual.md
index a92e45c26f..a654cfd8f9 100644
--- a/std/manual.md
+++ b/std/manual.md
@@ -394,7 +394,6 @@ const p = Deno.run({
     "run",
     "--allow-read",
     "https://deno.land/std/examples/cat.ts",
-    "--",
     ...fileNames
   ],
   stdout: "piped",
diff --git a/std/prettier/main_test.ts b/std/prettier/main_test.ts
index 0a7a05a461..5e9c0ad57e 100644
--- a/std/prettier/main_test.ts
+++ b/std/prettier/main_test.ts
@@ -25,8 +25,7 @@ const cmd = [
   "--allow-run",
   "--allow-write",
   "--allow-read",
-  "./prettier/main.ts",
-  "--"
+  "./prettier/main.ts"
 ];
 
 const testdata = join("prettier", "testdata");
@@ -403,7 +402,6 @@ test(async function testPrettierWithAutoConfig(): Promise<void> {
         "--allow-read",
         "--allow-env",
         prettierFile,
-        "--",
         "../5.ts",
         "--config",
         "auto"
@@ -470,7 +468,6 @@ test(async function testPrettierWithSpecifiedConfig(): Promise<void> {
         "--allow-read",
         "--allow-env",
         prettierFile,
-        "--",
         "../5.ts",
         "--config",
         config.name
@@ -506,7 +503,6 @@ test(async function testPrettierWithAutoIgnore(): Promise<void> {
       "--allow-read",
       "--allow-env",
       prettierFile,
-      "--",
       "**/*",
       "--ignore-path",
       "auto"
@@ -535,7 +531,6 @@ test(async function testPrettierWithSpecifiedIgnore(): Promise<void> {
       "--allow-read",
       "--allow-env",
       prettierFile,
-      "--",
       "**/*",
       "--ignore-path",
       "typescript.prettierignore"
diff --git a/test_plugin/tests/integration_tests.rs b/test_plugin/tests/integration_tests.rs
index 58aaccd849..cb76ef3ef4 100644
--- a/test_plugin/tests/integration_tests.rs
+++ b/test_plugin/tests/integration_tests.rs
@@ -26,7 +26,6 @@ fn basic() {
   let output = deno_cmd()
     .arg("--allow-plugin")
     .arg("tests/test.js")
-    .arg("--")
     .arg(BUILD_VARIANT)
     .output()
     .unwrap();
diff --git a/tools/http_benchmark.py b/tools/http_benchmark.py
index 2c552cf478..03f9f43654 100755
--- a/tools/http_benchmark.py
+++ b/tools/http_benchmark.py
@@ -35,7 +35,7 @@ def get_port(port=None):
 def deno_tcp(deno_exe):
     port = get_port()
     deno_cmd = [
-        deno_exe, "run", "--allow-net", "tools/deno_tcp.ts", "--",
+        deno_exe, "run", "--allow-net", "tools/deno_tcp.ts",
         server_addr(port)
     ]
     print "http_benchmark testing DENO tcp."
@@ -46,7 +46,7 @@ def deno_tcp_current_thread(deno_exe):
     port = get_port()
     deno_cmd = [
         deno_exe, "run", "--current-thread", "--allow-net",
-        "tools/deno_tcp.ts", "--",
+        "tools/deno_tcp.ts",
         server_addr(port)
     ]
     print "http_benchmark testing DENO tcp (single-thread)."
@@ -56,7 +56,7 @@ def deno_tcp_current_thread(deno_exe):
 def deno_http(deno_exe):
     port = get_port()
     deno_cmd = [
-        deno_exe, "run", "--allow-net", "std/http/http_bench.ts", "--",
+        deno_exe, "run", "--allow-net", "std/http/http_bench.ts",
         server_addr(port)
     ]
     print "http_benchmark testing DENO using net/http."
@@ -67,7 +67,7 @@ def deno_tcp_proxy(deno_exe, hyper_hello_exe):
     port = get_port()
     origin_port = get_port()
     deno_cmd = [
-        deno_exe, "run", "--allow-net", "tools/deno_tcp_proxy.ts", "--",
+        deno_exe, "run", "--allow-net", "tools/deno_tcp_proxy.ts",
         server_addr(port),
         server_addr(origin_port)
     ]
@@ -82,7 +82,7 @@ def deno_http_proxy(deno_exe, hyper_hello_exe):
     port = get_port()
     origin_port = get_port()
     deno_cmd = [
-        deno_exe, "run", "--allow-net", "tools/deno_http_proxy.ts", "--",
+        deno_exe, "run", "--allow-net", "tools/deno_http_proxy.ts",
         server_addr(port),
         server_addr(origin_port)
     ]
diff --git a/tools/throughput_benchmark.py b/tools/throughput_benchmark.py
index 4e285a7b8b..f46503193f 100755
--- a/tools/throughput_benchmark.py
+++ b/tools/throughput_benchmark.py
@@ -21,7 +21,7 @@ def cat(deno_exe, megs):
     size = megs * MB
     start = time.time()
     cmd = deno_exe + " run --allow-read "
-    cmd += "tests/cat.ts -- /dev/zero | head -c %s " % size
+    cmd += "tests/cat.ts /dev/zero | head -c %s " % size
     print cmd
     subprocess.check_output(cmd, shell=True)
     end = time.time()
@@ -32,8 +32,7 @@ def tcp(deno_exe, megs):
     size = megs * MB
     # Run deno echo server in the background.
     args = [
-        deno_exe, "run", "--allow-net", "tests/echo_server.ts", "--",
-        SERVER_ADDR
+        deno_exe, "run", "--allow-net", "tests/echo_server.ts", SERVER_ADDR
     ]
     print args
     echo_server = subprocess.Popen(args)