diff --git a/app/atom_main_delegate.cc b/app/atom_main_delegate.cc
index 1f3d9cb69039..47718e22baa3 100644
--- a/app/atom_main_delegate.cc
+++ b/app/atom_main_delegate.cc
@@ -54,6 +54,9 @@ void AtomMainDelegate::PreSandboxStartup() {
   // Disable accelerated compositing since it caused a lot of troubles (black
   // devtools, screen flashes) and needed lots of effort to make it right.
   command_line->AppendSwitch(switches::kDisableAcceleratedCompositing);
+
+  // Add a flag to mark the end of switches added by atom-shell.
+  command_line->AppendSwitch("no-more-switches");
 }
 
 void AtomMainDelegate::InitializeResourceBundle() {
diff --git a/atom.gyp b/atom.gyp
index 3a03dd51165b..63562cfa4e71 100644
--- a/atom.gyp
+++ b/atom.gyp
@@ -21,15 +21,15 @@
       'browser/api/lib/menu-item.coffee',
       'browser/api/lib/power-monitor.coffee',
       'browser/api/lib/protocol.coffee',
-      'browser/atom/atom.coffee',
-      'browser/atom/atom-renderer.coffee',
-      'browser/atom/objects-registry.coffee',
-      'browser/atom/rpc-server.coffee',
+      'browser/lib/init.coffee',
+      'browser/lib/objects-registry.coffee',
+      'browser/lib/rpc-server.coffee',
       'common/api/lib/callbacks-registry.coffee',
       'common/api/lib/clipboard.coffee',
       'common/api/lib/crash-reporter.coffee',
       'common/api/lib/id-weak-map.coffee',
       'common/api/lib/shell.coffee',
+      'renderer/lib/init.coffee',
       'renderer/api/lib/ipc.coffee',
       'renderer/api/lib/remote.coffee',
     ],
diff --git a/browser/api/lib/app.coffee b/browser/api/lib/app.coffee
index 9fc9664ed423..e578c3ef7d3c 100644
--- a/browser/api/lib/app.coffee
+++ b/browser/api/lib/app.coffee
@@ -10,7 +10,7 @@ app.getHomeDir = ->
   process.env[if process.platform is 'win32' then 'USERPROFILE' else 'HOME']
 
 app.getBrowserWindows = ->
-  require('../../atom/objects-registry.js').getAllWindows()
+  require('../../lib/objects-registry.js').getAllWindows()
 
 app.setApplicationMenu = (menu) ->
   require('menu').setApplicationMenu menu
diff --git a/browser/atom/atom-renderer.coffee b/browser/atom/atom-renderer.coffee
deleted file mode 100644
index 8430d183340d..000000000000
--- a/browser/atom/atom-renderer.coffee
+++ /dev/null
@@ -1,5 +0,0 @@
-path = require 'path'
-
-process.__atom_type = 'renderer'
-process.resourcesPath = path.resolve process.argv[1], '..', '..', '..'
-process.argv.splice 1, 1
diff --git a/browser/atom_browser_main_parts.cc b/browser/atom_browser_main_parts.cc
index 2328fda1bb29..3c3b2e70196e 100644
--- a/browser/atom_browser_main_parts.cc
+++ b/browser/atom_browser_main_parts.cc
@@ -43,9 +43,19 @@ void AtomBrowserMainParts::PostEarlyInitialization() {
 
   node_bindings_->Initialize();
 
-  // Wrap whole process in one global context.
-  global_env->context()->Enter();
+  v8::V8::Initialize();
 
+  // Create context.
+  v8::HandleScope handle_scope(node_isolate);
+  v8::Local<v8::Context> context = v8::Context::New(node_isolate);
+
+  // Wrap whole process in one global context.
+  context->Enter();
+
+  // Create the global environment.
+  global_env = node_bindings_->CreateEnvironment(context);
+
+  // Add atom-shell extended APIs.
   atom_bindings_->BindTo(global_env->process_object());
   atom_bindings_->AfterLoad();
 }
diff --git a/browser/atom/atom.coffee b/browser/lib/init.coffee
similarity index 94%
rename from browser/atom/atom.coffee
rename to browser/lib/init.coffee
index 6212dd0b2959..a9393f16aa5d 100644
--- a/browser/atom/atom.coffee
+++ b/browser/lib/init.coffee
@@ -1,9 +1,12 @@
 fs = require 'fs'
 path = require 'path'
 
-# Restore the proces.argv.
+# Expose information of current process.
 process.__atom_type = 'browser'
 process.resourcesPath = path.resolve process.argv[1], '..', '..', '..'
+
+# We modified the original process.argv to let node.js load the atom.js,
+# we need to restore it here.
 process.argv.splice 1, 1
 
 if process.platform is 'win32'
diff --git a/browser/atom/objects-registry.coffee b/browser/lib/objects-registry.coffee
similarity index 100%
rename from browser/atom/objects-registry.coffee
rename to browser/lib/objects-registry.coffee
diff --git a/browser/atom/rpc-server.coffee b/browser/lib/rpc-server.coffee
similarity index 100%
rename from browser/atom/rpc-server.coffee
rename to browser/lib/rpc-server.coffee
diff --git a/common/node_bindings.cc b/common/node_bindings.cc
index 9bda801b95f2..a2fe827d71a0 100644
--- a/common/node_bindings.cc
+++ b/common/node_bindings.cc
@@ -13,9 +13,6 @@
 #include "base/path_service.h"
 #include "common/v8/native_type_conversions.h"
 #include "content/public/browser/browser_thread.h"
-#include "net/base/escape.h"
-#include "third_party/WebKit/public/web/WebDocument.h"
-#include "third_party/WebKit/public/web/WebFrame.h"
 #include "vendor/node/src/node_javascript.h"
 
 #if defined(OS_WIN)
@@ -28,24 +25,42 @@ using content::BrowserThread;
 
 // Forward declaration of internal node functions.
 namespace node {
-void Init(int* argc,
-          const char** argv,
-          int* exec_argc,
-          const char*** exec_argv);
-Environment* CreateEnvironment(v8::Isolate* isolate,
-                               int argc,
-                               const char* const* argv,
-                               int exec_argc,
-                               const char* const* exec_argv);
+void Init(int*, const char**, int*, const char***);
+void Load(Environment* env);
+void SetupProcessObject(Environment*, int, const char* const*, int,
+                        const char* const*);
 }
 
 namespace atom {
 
 namespace {
 
+// Empty callback for async handle.
 void UvNoOp(uv_async_t* handle, int status) {
 }
 
+// Convert the given vector to an array of C-strings. The strings in the
+// returned vector are only guaranteed valid so long as the vector of strings
+// is not modified.
+scoped_ptr<const char*[]> StringVectorToArgArray(
+    const std::vector<std::string>& vector) {
+  scoped_ptr<const char*[]> array(new const char*[vector.size()]);
+  for (size_t i = 0; i < vector.size(); ++i)
+    array[i] = vector[i].c_str();
+  return array.Pass();
+}
+
+#if defined(OS_WIN)
+std::vector<std::string> String16VectorToStringVector(
+    const std::vector<string16>& vector) {
+  std::vector<std::string> utf8_vector;
+  utf8_vector.reserve(vector.size());
+  for (size_t i = 0; i < vector.size(); ++i)
+    utf8_vector.push_back(UTF16ToUTF8(vector[i]));
+  return utf8_vector;
+}
+#endif
+
 }  // namespace
 
 node::Environment* global_env = NULL;
@@ -73,42 +88,6 @@ NodeBindings::~NodeBindings() {
 }
 
 void NodeBindings::Initialize() {
-  CommandLine::StringVector str_argv = CommandLine::ForCurrentProcess()->argv();
-
-#if defined(OS_WIN)
-  std::vector<std::string> utf8_str_argv;
-  utf8_str_argv.reserve(str_argv.size());
-#endif
-
-  // Convert string vector to const char* array.
-  std::vector<const char*> args(str_argv.size(), NULL);
-  for (size_t i = 0; i < str_argv.size(); ++i) {
-#if defined(OS_WIN)
-    utf8_str_argv.push_back(UTF16ToUTF8(str_argv[i]));
-    args[i] = utf8_str_argv[i].c_str();
-#else
-    args[i] = str_argv[i].c_str();
-#endif
-  }
-
-  // Feed node the path to initialization script.
-  base::FilePath exec_path(str_argv[0]);
-  PathService::Get(base::FILE_EXE, &exec_path);
-  base::FilePath resources_path =
-#if defined(OS_MACOSX)
-      is_browser_ ? exec_path.DirName().DirName().Append("Resources") :
-                    exec_path.DirName().DirName().DirName().DirName().DirName()
-                             .Append("Resources");
-#else
-      exec_path.DirName().Append("resources");
-#endif
-  base::FilePath script_path =
-      resources_path.AppendASCII("browser")
-                    .AppendASCII("atom")
-                    .AppendASCII(is_browser_ ? "atom.js" : "atom-renderer.js");
-  std::string script_path_str = script_path.AsUTF8Unsafe();
-  args.insert(args.begin() + 1, script_path_str.c_str());
-
   // Init idle GC for browser.
   if (is_browser_) {
     uv_timer_init(uv_default_loop(), &idle_timer_);
@@ -120,43 +99,76 @@ void NodeBindings::Initialize() {
   node::g_upstream_node_mode = false;
 
   // Init node.
-  int argc = args.size();
-  const char** argv = &args[0];
-  int exec_argc;
-  const char** exec_argv;
-  node::Init(&argc, argv, &exec_argc, &exec_argv);
-  v8::V8::Initialize();
-
-  // Create environment (setup process object and load node.js).
-  global_env = node::CreateEnvironment(node_isolate, argc, argv, argc, argv);
+  // (we assume it would not node::Init would not modify the parameters under
+  // embedded mode).
+  node::Init(NULL, NULL, NULL, NULL);
 }
 
-void NodeBindings::BindTo(WebKit::WebFrame* frame) {
-  v8::HandleScope handle_scope(node_isolate);
+node::Environment* NodeBindings::CreateEnvironment(
+    v8::Handle<v8::Context> context) {
+  std::vector<std::string> args =
+#if defined(OS_WIN)
+      String16VectorToStringVector(CommandLine::ForCurrentProcess()->argv());
+#else
+      CommandLine::ForCurrentProcess()->argv();
+#endif
 
-  v8::Handle<v8::Context> context = frame->mainWorldScriptContext();
-  if (context.IsEmpty())
-    return;
+  // Feed node the path to initialization script.
+  base::FilePath exec_path(args[0]);
+  PathService::Get(base::FILE_EXE, &exec_path);
+  base::FilePath resources_path =
+#if defined(OS_MACOSX)
+      is_browser_ ? exec_path.DirName().DirName().Append("Resources") :
+                    exec_path.DirName().DirName().DirName().DirName().DirName()
+                             .Append("Resources");
+#else
+      exec_path.DirName().Append("resources");
+#endif
+  base::FilePath script_path =
+      resources_path.AppendASCII(is_browser_ ? "browser" : "renderer")
+                    .AppendASCII("lib")
+                    .AppendASCII("init.js");
+  std::string script_path_str = script_path.AsUTF8Unsafe();
+  args.insert(args.begin() + 1, script_path_str.c_str());
 
-  v8::Context::Scope scope(context);
+  // Convert string vector to const char* array.
+  scoped_ptr<const char*[]> c_argv = StringVectorToArgArray(args);
 
-  // Erase security token.
-  context->SetSecurityToken(global_env->context()->GetSecurityToken());
+  // Construct the parameters that passed to node::CreateEnvironment:
+  v8::Isolate* isolate = context->GetIsolate();
+  int argc = args.size();
+  const char** argv = c_argv.get();
+  int exec_argc = 0;
+  const char** exec_argv = NULL;
 
-  // Evaluate cefode.js.
-  v8::Handle<v8::Script> script = node::CompileCefodeMainSource();
-  v8::Local<v8::Value> result = script->Run();
+  using namespace v8;  // NOLINT
+  using namespace node;  // NOLINT
 
-  // Run the script of cefode.js.
-  std::string script_path(GURL(frame->document().url()).path());
-  script_path = net::UnescapeURLComponent(
-      script_path,
-      net::UnescapeRule::SPACES | net::UnescapeRule::URL_SPECIAL_CHARS);
-  v8::Handle<v8::Value> args[2] = {
-    global_env->process_object(),
-    ToV8Value(script_path),
-  };
-  v8::Local<v8::Function>::Cast(result)->Call(context->Global(), 2, args);
+  // Following code are stripped from node::CreateEnvironment in node.cc:
+  HandleScope handle_scope(isolate);
+
+  Environment* env = Environment::New(context);
+
+  uv_check_init(env->event_loop(), env->immediate_check_handle());
+  uv_unref(
+      reinterpret_cast<uv_handle_t*>(env->immediate_check_handle()));
+  uv_idle_init(env->event_loop(), env->immediate_idle_handle());
+
+  uv_prepare_init(env->event_loop(), env->idle_prepare_handle());
+  uv_check_init(env->event_loop(), env->idle_check_handle());
+  uv_unref(reinterpret_cast<uv_handle_t*>(env->idle_prepare_handle()));
+  uv_unref(reinterpret_cast<uv_handle_t*>(env->idle_check_handle()));
+
+  Local<FunctionTemplate> process_template = FunctionTemplate::New();
+  process_template->SetClassName(FIXED_ONE_BYTE_STRING(isolate, "process"));
+
+  Local<Object> process_object = process_template->GetFunction()->NewInstance();
+  env->set_process_object(process_object);
+
+  SetupProcessObject(env, argc, argv, exec_argc, exec_argv);
+  Load(env);
+
+  return env;
 }
 
 void NodeBindings::PrepareMessageLoop() {
diff --git a/common/node_bindings.h b/common/node_bindings.h
index a9ac5852a129..7ed22806d115 100644
--- a/common/node_bindings.h
+++ b/common/node_bindings.h
@@ -2,20 +2,21 @@
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
-#ifndef RAVE_COMMON_NODE_BINDINGS_
-#define RAVE_COMMON_NODE_BINDINGS_
+#ifndef ATOM_COMMON_NODE_BINDINGS_H_
+#define ATOM_COMMON_NODE_BINDINGS_H_
 
 #include "base/basictypes.h"
+#include "v8/include/v8.h"
 #include "vendor/node/deps/uv/include/uv.h"
 
-namespace WebKit {
-class WebFrame;
-}
-
 namespace base {
 class MessageLoop;
 }
 
+namespace node {
+class Environment;
+}
+
 namespace atom {
 
 class NodeBindings {
@@ -24,11 +25,11 @@ class NodeBindings {
 
   virtual ~NodeBindings();
 
-  // Setup V8, libuv and the process object, then load the node.js script.
+  // Setup V8, libuv.
   virtual void Initialize();
 
-  // Load cefode.js script under web frame.
-  virtual void BindTo(WebKit::WebFrame* frame);
+  // Create the environment and load node.js.
+  virtual node::Environment* CreateEnvironment(v8::Handle<v8::Context> context);
 
   // Prepare for message loop integration.
   virtual void PrepareMessageLoop();
@@ -87,4 +88,4 @@ class NodeBindings {
 
 }  // namespace atom
 
-#endif  // RAVE_COMMON_NODE_BINDINGS_
+#endif  // ATOM_COMMON_NODE_BINDINGS_H_
diff --git a/common/v8/node_common.h b/common/v8/node_common.h
index 5b8147f93122..7174b902a59e 100644
--- a/common/v8/node_common.h
+++ b/common/v8/node_common.h
@@ -5,7 +5,7 @@
 #ifndef ATOM_COMMON_V8_NODE_COMMON_H_
 #define ATOM_COMMON_V8_NODE_COMMON_H_
 
-// Common helper for using node APIs.
+// Include common headers for using node APIs.
 
 #undef CHECK
 #undef DISALLOW_COPY_AND_ASSIGN
@@ -16,6 +16,8 @@ using node::node_isolate;
 
 namespace atom {
 // Defined in node_bindings.cc.
+// For renderer it's created in atom_renderer_client.cc.
+// For browser it's created in atom_browser_main_parts.cc.
 extern node::Environment* global_env;
 }
 
diff --git a/renderer/atom_render_view_observer.cc b/renderer/atom_render_view_observer.cc
index dd4dfbe553db..673435e048e1 100644
--- a/renderer/atom_render_view_observer.cc
+++ b/renderer/atom_render_view_observer.cc
@@ -4,9 +4,6 @@
 
 #include "renderer/atom_render_view_observer.h"
 
-#include <algorithm>
-#include <vector>
-
 #include "common/api/api_messages.h"
 #include "common/node_bindings.h"
 #include "ipc/ipc_message_macros.h"
@@ -15,69 +12,47 @@
 #include "third_party/WebKit/public/web/WebDocument.h"
 #include "third_party/WebKit/public/web/WebDraggableRegion.h"
 #include "third_party/WebKit/public/web/WebFrame.h"
-#include "v8/include/v8.h"
+
+#include "common/v8/node_common.h"
 
 using WebKit::WebFrame;
 
-namespace webkit {
-extern void SetGetFirstWindowContext(v8::Handle<v8::Context> (*)());
-extern void SetIsValidWindowContext(bool (*)(v8::Handle<v8::Context>));
-}
-
 namespace atom {
 
-namespace {
-
-std::vector<WebFrame*>& web_frames() {
-  CR_DEFINE_STATIC_LOCAL(std::vector<WebFrame*>, frames, ());
-  return frames;
-}
-
-v8::Handle<v8::Context> GetFirstWindowContext() {
-  if (web_frames().size() == 0)
-    return v8::Handle<v8::Context>();
-
-  return web_frames()[0]->mainWorldScriptContext();
-}
-
-bool IsValidWindowContext(v8::Handle<v8::Context> context) {
-  size_t size = web_frames().size();
-  for (size_t i = 0; i < size; ++i)
-    if (web_frames()[i]->mainWorldScriptContext() == context)
-      return true;
-
-  return false;
-}
-
-}  // namespace
-
 AtomRenderViewObserver::AtomRenderViewObserver(
     content::RenderView* render_view,
     AtomRendererClient* renderer_client)
     : content::RenderViewObserver(render_view),
       atom_bindings_(new AtomRendererBindings(render_view)),
       renderer_client_(renderer_client) {
-  // Interact with dirty workarounds of extra node context in WebKit.
-  webkit::SetGetFirstWindowContext(GetFirstWindowContext);
-  webkit::SetIsValidWindowContext(IsValidWindowContext);
 }
 
 AtomRenderViewObserver::~AtomRenderViewObserver() {
 }
 
 void AtomRenderViewObserver::DidClearWindowObject(WebFrame* frame) {
-  // Remember the web frame.
-  web_frames().push_back(frame);
+  // Get the context.
+  v8::HandleScope handle_scope(node_isolate);
+  v8::Handle<v8::Context> context = frame->mainWorldScriptContext();
+  if (context.IsEmpty())
+    return;
 
-  renderer_client_->node_bindings()->BindTo(frame);
+  v8::Context::Scope scope(context);
+
+  // Check the existance of process object to prevent duplicate initialization.
+  if (context->Global()->Has(v8::String::New("process")))
+    return;
+
+  // Give the node loop a run to make sure everything is ready.
+  renderer_client_->node_bindings()->RunMessageLoop();
+
+  // Setup node environment for each window.
+  renderer_client_->node_bindings()->CreateEnvironment(context);
+
+  // Add atom-shell extended APIs.
   atom_bindings()->BindToFrame(frame);
 }
 
-void AtomRenderViewObserver::FrameWillClose(WebFrame* frame) {
-  std::vector<WebFrame*>& vec = web_frames();
-  vec.erase(std::remove(vec.begin(), vec.end(), frame), vec.end());
-}
-
 void AtomRenderViewObserver::DraggableRegionsChanged(WebKit::WebFrame* frame) {
   WebKit::WebVector<WebKit::WebDraggableRegion> webregions =
       frame->document().draggableRegions();
diff --git a/renderer/atom_render_view_observer.h b/renderer/atom_render_view_observer.h
index d8d90e0cb4b1..12c15fa63675 100644
--- a/renderer/atom_render_view_observer.h
+++ b/renderer/atom_render_view_observer.h
@@ -28,7 +28,6 @@ class AtomRenderViewObserver : content::RenderViewObserver {
   virtual ~AtomRenderViewObserver();
 
   virtual void DidClearWindowObject(WebKit::WebFrame*) OVERRIDE;
-  virtual void FrameWillClose(WebKit::WebFrame*) OVERRIDE;
 
  private:
   // content::RenderViewObserver implementation.
diff --git a/renderer/atom_renderer_client.cc b/renderer/atom_renderer_client.cc
index 183d2d57ca4c..3574b02cacad 100644
--- a/renderer/atom_renderer_client.cc
+++ b/renderer/atom_renderer_client.cc
@@ -9,20 +9,8 @@
 
 #include "common/v8/node_common.h"
 
-namespace webkit {
-extern void SetGetNodeContext(v8::Handle<v8::Context> (*)());
-}
-
 namespace atom {
 
-namespace {
-
-v8::Handle<v8::Context> GetNodeContext() {
-  return global_env->context();
-}
-
-}  // namespace
-
 AtomRendererClient::AtomRendererClient()
     : node_bindings_(NodeBindings::Create(false)) {
 }
@@ -32,12 +20,15 @@ AtomRendererClient::~AtomRendererClient() {
 
 void AtomRendererClient::RenderThreadStarted() {
   node_bindings_->Initialize();
-
-  // Interact with dirty workarounds of extra node context in WebKit.
-  webkit::SetGetNodeContext(GetNodeContext);
-
   node_bindings_->PrepareMessageLoop();
-  node_bindings_->RunMessageLoop();
+
+  DCHECK(!global_env);
+
+  // Create a default empty environment which would be used when we need to
+  // run V8 code out of a window context (like running a uv callback).
+  v8::HandleScope handle_scope(node_isolate);
+  v8::Local<v8::Context> context = v8::Context::New(node_isolate);
+  global_env = node::Environment::New(context);
 }
 
 void AtomRendererClient::RenderViewCreated(content::RenderView* render_view) {
diff --git a/renderer/lib/init.coffee b/renderer/lib/init.coffee
new file mode 100644
index 000000000000..8a14c69128d1
--- /dev/null
+++ b/renderer/lib/init.coffee
@@ -0,0 +1,23 @@
+path = require 'path'
+
+# Expose information of current process.
+process.__atom_type = 'renderer'
+process.resourcesPath = path.resolve process.argv[1], '..', '..', '..'
+
+# We modified the original process.argv to let node.js load the
+# atom-renderer.js, we need to restore it here.
+process.argv.splice 1, 1
+
+# Add renderer/api/lib to require's search paths, which contains javascript part
+# of Atom's built-in libraries.
+globalPaths = require('module').globalPaths
+globalPaths.push path.join process.resourcesPath, 'renderer', 'api', 'lib'
+
+# And also common/api/lib
+globalPaths.push path.join process.resourcesPath, 'common', 'api', 'lib'
+
+# Expose global variables.
+global.require = require
+global.module = module
+global.__filename = __filename
+global.__dirname = __dirname
diff --git a/vendor/node b/vendor/node
index 9a7dea685069..2fce49829b4d 160000
--- a/vendor/node
+++ b/vendor/node
@@ -1 +1 @@
-Subproject commit 9a7dea6850695c4a7c783c721aec0d4e5f1245b4
+Subproject commit 2fce49829b4dde69bceed91c00cec578517541b0