diff --git a/core/includes/theme.inc b/core/includes/theme.inc
index 5f4bcdb..cd59f95 100644
--- a/core/includes/theme.inc
+++ b/core/includes/theme.inc
@@ -1056,47 +1056,42 @@ function theme($hook, $variables = array()) {
     }
   }
 
-  // Provide context for hooks.
-  $context = array(
-    '#theme_id' => $original_hook,
-    '#base_theme_id' => $hook,
-    '#suggestions' => $suggestions,
+  // Provide immutable context for subsequent hooks.
+  $context_original = array(
+    'hook' => $hook,
+    'original_hook' => $original_hook,
+    'suggestions' => $suggestions,
   );
 
-  $invoke_hooks = array(
+  // A list of hooks that we'll fire for the given theme hook.
+  $prepare_hooks = array(
     'theme_prepare',
     'theme_prepare_' . $hook,
   );
   // If the original theme hook is not the same as the base theme hook, then
   // invoke the original theme hook suggestion after the base theme hook.
   if ($hook !== $original_hook) {
-    $invoke_hooks[] = 'theme_prepare_' . $original_hook;
+    $prepare_hooks[] = 'theme_prepare_' . $original_hook;
   }
 
-  // Invoke theme_prepare hooks for enabled modules.
-  foreach ($invoke_hooks as $invoke_hook) {
-    $variables = NestedArray::mergeDeep($variables, (array) Drupal::moduleHandler()->invokeAll($invoke_hook, array($context)));
-  }
-
-  // Invoke hooks for the active theme. The active theme takes precedence over
+  // Invokes hook_theme_prepare(), hook_theme_prepare_THEME_ID() for enabled
   // modules.
-  // @todo Replace with Drupal::themeHandler()->invoke() once implemented.
-  // @see https://drupal.org/node/2029819
-  foreach ($invoke_hooks as $invoke_hook) {
-    $variables = NestedArray::mergeDeep($variables, (array) Drupal::moduleHandler()->themeInvoke($invoke_hook, array($context)));
+  foreach ($prepare_hooks as $prepare_hook) {
+    $context = $context_original;
+    $variables = NestedArray::mergeDeep($variables, (array) Drupal::moduleHandler()->invokeAll($prepare_hook, array($context)));
   }
 
-  // Clone the context so it cannot be altered by modules or themes.
-  $context_clone = $context;
-
-  // Invoke alter hooks for enabled modules.
-  // @todo Add Drupal::themeHandler()->alter() invocations once implemented.
+  // Invokes hook_theme_prepare(), hook_theme_prepare_THEME_ID() for the active
+  // theme, which takes precedence over modules.
+  // @todo Replace with Drupal::themeHandler()->invoke() once implemented.
   // @see https://drupal.org/node/2029819
-  foreach ($invoke_hooks as $invoke_hook) {
-    Drupal::moduleHandler()->alter($invoke_hook, $variables, $context_clone);
+  foreach ($prepare_hooks as $prepare_hook) {
+    $context = $context_original;
+    $variables = NestedArray::mergeDeep($variables, (array) Drupal::moduleHandler()->themeInvoke($prepare_hook, array($context)));
   }
 
-  // @todo Deprecate https://drupal.org/node/2060773
+  // Invokes preprocess functions.
+  // @todo Deprecate @see https://drupal.org/node/2060773
   if (isset($info['preprocess functions'])) {
     foreach ($info['preprocess functions'] as $preprocessor_function) {
       if (function_exists($preprocessor_function)) {
@@ -1105,6 +1100,14 @@ function theme($hook, $variables = array()) {
     }
   }
 
+  // Invokes hook_theme_prepare_alter(), hook_theme_prepare_THEME_ID_alter() for enabled modules.
+  // @todo Add Drupal::themeHandler()->alter() invocations once implemented.
+  // @see https://drupal.org/node/2029819
+  foreach ($prepare_hooks as $prepare_hook) {
+    $context = $context_original;
+    Drupal::moduleHandler()->alter($prepare_hook, $variables, $context);
+  }
+
   // Generate the output using either a function or a template.
   $output = '';
   if (isset($info['function'])) {
diff --git a/core/lib/Drupal/Core/Extension/UpdateModuleHandler.php b/core/lib/Drupal/Core/Extension/UpdateModuleHandler.php
index 34c6793..7d7ac9c 100644
--- a/core/lib/Drupal/Core/Extension/UpdateModuleHandler.php
+++ b/core/lib/Drupal/Core/Extension/UpdateModuleHandler.php
@@ -24,10 +24,6 @@ public function getImplementations($hook) {
     if (substr($hook, -6) === '_alter') {
       return array();
     }
-    // Some system_theme() hooks need to be prepared.
-    if (substr($hook, 0, 13) === 'theme_prepare') {
-      return array('system');
-    }
     // theme() is called during updates and fires hooks, so whitelist the
     // system module.
     if (substr($hook, 0, 6) == 'theme_') {
diff --git a/core/modules/system/lib/Drupal/system/Tests/Theme/ThemePrepareTest.php b/core/modules/system/lib/Drupal/system/Tests/Theme/ThemePrepareTest.php
index d8a7451..8b1ed5d 100644
--- a/core/modules/system/lib/Drupal/system/Tests/Theme/ThemePrepareTest.php
+++ b/core/modules/system/lib/Drupal/system/Tests/Theme/ThemePrepareTest.php
@@ -2,16 +2,15 @@
 
 /**
  * @file
- * Definition of Drupal\system\Tests\Theme\ThemeTest.
+ * Definition of Drupal\system\Tests\Theme\ThemePrepareTest.
  */
 
 namespace Drupal\system\Tests\Theme;
 
 use Drupal\simpletest\WebTestBase;
-use Drupal\test_theme\ThemeClass;
 
 /**
- * Tests low-level theme functions.
+ * Tests hook_theme_prepare() and hook_theme_prepare_alter() implementations.
  */
 class ThemePrepareTest extends WebTestBase {
 
@@ -36,19 +35,19 @@ function setUp() {
   }
 
   function testThemePrepare() {
-    $this->drupalGet('theme-test/prepare', array('query' => array('XDEBUG_SESSION_START' => 'PHPSTORM')));
-    $this->assertText('Inserted variable1 via hook_theme_prepare().', 'Inserted variable1 via hook_theme_prepare().');
-    $this->assertText('Inserted variable2 via hook_theme_prepare_BASE_THEME_ID().', 'Inserted variable2 via hook_theme_prepare_BASE_THEME_ID().');
-    $this->assertText('Inserted themeVariable1 via theme hook_theme_prepare().', 'Inserted themeVariable1 via theme hook_theme_prepare().');
-    $this->assertText('Inserted themeVariable2 via theme hook_theme_prepare_BASE_THEME_ID().', 'Inserted themeVariable2 via theme hook_theme_prepare_BASE_THEME_ID().');
+    $this->drupalGet('theme-test/prepare');
+    $this->assertText('Inserted variable1 via hook_theme_prepare().');
+    $this->assertText('Inserted variable2 via hook_theme_prepare_BASE_THEME_ID().');
+    $this->assertText('Inserted themeVariable1 via theme hook_theme_prepare().');
+    $this->assertText('Inserted themeVariable2 via theme hook_theme_prepare_BASE_THEME_ID().');
   }
 
   function testThemePrepareAlter() {
-    $this->drupalGet('theme-test/prepare-alter', array('query' => array('XDEBUG_SESSION_START' => 'PHPSTORM')));
-    $this->assertText('Inserted variable1 via hook_theme_prepare() was altered by hook_theme_prepare_alter().', 'Inserted variable1 via hook_theme_prepare() was altered by hook_theme_prepare_alter().');
-    $this->assertText('Inserted variable2 via hook_theme_prepare_BASE_THEME_ID() was altered by hook_theme_prepare_BASE_THEME_ID_alter().', 'Inserted variable2 via hook_theme_prepare_BASE_THEME_ID() was altered by hook_theme_prepare_BASE_THEME_ID_alter().');
-    $this->assertText('Inserted themeVariable1 via theme hook_theme_prepare() was altered by theme hook_theme_prepare_alter().', 'Inserted themeVariable1 via theme hook_theme_prepare() was altered by theme hook_theme_prepare_alter().');
-    $this->assertText('Inserted themeVariable2 via theme hook_theme_prepare_BASE_THEME_ID() was altered by theme hook_theme_prepare_BASE_THEME_ID_alter().', 'Inserted themeVariable2 via theme hook_theme_prepare_BASE_THEME_ID() was altered by theme hook_theme_prepare_BASE_THEME_ID_alter().');
+    $this->drupalGet('theme-test/prepare-alter');
+    $this->assertText('Inserted variable1 via hook_theme_prepare() was altered by hook_theme_prepare_alter().');
+    $this->assertText('Inserted variable2 via hook_theme_prepare_BASE_THEME_ID() was altered by hook_theme_prepare_BASE_THEME_ID_alter().');
+    $this->assertText('Inserted themeVariable1 via theme hook_theme_prepare() was altered by theme hook_theme_prepare_alter().');
+    $this->assertText('Inserted themeVariable2 via theme hook_theme_prepare_BASE_THEME_ID() was altered by theme hook_theme_prepare_BASE_THEME_ID_alter().');
   }
 
 }
diff --git a/core/modules/system/tests/modules/theme_test/lib/Drupal/theme_test/ThemeTestController.php b/core/modules/system/tests/modules/theme_test/lib/Drupal/theme_test/ThemeTestController.php
index 32231ff..1389cea 100644
--- a/core/modules/system/tests/modules/theme_test/lib/Drupal/theme_test/ThemeTestController.php
+++ b/core/modules/system/tests/modules/theme_test/lib/Drupal/theme_test/ThemeTestController.php
@@ -120,12 +120,18 @@ function functionSuggestionAlter() {
     return array('#theme' => 'theme_test_function_suggestions');
   }
 
+  /**
+   * Menu callback for testing hook_theme_prepare().
+   */
   function prepare() {
     return array(
       '#theme' => 'theme_test_prepare_variable',
     );
   }
 
+  /**
+   * Menu callback for testing hook_theme_prepare_alter().
+   */
   function prepareAlter() {
     return array(
       '#theme' => 'theme_test_prepare_alter_variable',