Index: wp-admin/includes/ms.php
===================================================================
--- wp-admin/includes/ms.php	(revision 12614)
+++ wp-admin/includes/ms.php	(working copy)
@@ -549,34 +549,8 @@
 add_action( 'admin_page_access_denied', 'redirect_user_to_blog', 99 );
 
 function wpmu_menu() {
-	global $menu, $submenu, $current_user;
-
-	$menu_perms = get_site_option( "menu_items" );
-	if( is_array( $menu_perms ) == false )
-		$menu_perms = array();
-	if( $menu_perms[ 'plugins' ] != 1 ) {
-		if( !is_site_admin() ) {
-			unset( $menu['65'] ); // Plugins
-			unset( $submenu[ 'plugins.php' ] );
-		} elseif ( strpos( $_SERVER[ 'PHP_SELF' ], 'wp-admin/plugins.php' ) ) {
-			$message = sprintf( __( 'The plugins page is not visible to normal users. It must be activated first. %s' ), '<a href="wpmu-options.php#menu">' . __( 'Activate' ) . '</a>' );
-			$message = str_replace( "'", "\'", "<div class='error'><p>$message</p></div>" );
-			add_action( 'admin_notices', create_function( '', "echo '$message';" ) );
-		}
-	} elseif ( !is_site_admin() ) {
-		$menu[65] = array( sprintf( __('Plugins %s'), "" ), 'activate_plugins', 'plugins.php', '', 'menu-top', 'menu-plugins', 'div' );
-	}
-	if( !get_site_option( 'add_new_users' ) ) {
-		if( !is_site_admin() ) {
-			unset( $submenu['users.php'][10] );
-		} else {
-			$submenu['users.php'][10] = array(__('Add New') . ' <strong>*</strong>', 'create_users', 'wpmu-options.php#addnewusers');
-		}
-	}
-	unset( $submenu['tools.php'][20] ); // core upgrade
-	unset( $submenu['options-general.php'][45] ); // Misc
+	// deprecated. See #11763
 }
-add_action( '_admin_menu', 'wpmu_menu' );
 
 function mu_options( $options ) {
 	if ( defined( 'POST_BY_EMAIL' ) ) {
Index: wp-admin/menu.php
===================================================================
--- wp-admin/menu.php	(revision 12614)
+++ wp-admin/menu.php	(working copy)
@@ -109,14 +109,17 @@
 if ( !empty($update_plugins->response) )
 	$update_count = count( $update_plugins->response );
 
-$menu[65] = array( sprintf( __('Plugins %s'), "<span class='update-plugins count-$update_count'><span class='plugin-count'>" . number_format_i18n($update_count) . "</span></span>" ), 'activate_plugins', 'plugins.php', '', 'menu-top', 'menu-plugins', 'div' );
-	$submenu['plugins.php'][5]  = array( __('Installed'), 'activate_plugins', 'plugins.php' );
-	if ( is_super_admin() ) {
-		/* translators: add new plugin */
-		$submenu['plugins.php'][10] = array(_x('Add New', 'plugin'), 'install_plugins', 'plugin-install.php');
-	}
-	if ( !is_multisite() )
-		$submenu['plugins.php'][15] = array( __('Editor'), 'edit_plugins', 'plugin-editor.php' );
+$menu_perms = get_site_option('menu_items', array());
+if ( is_super_admin() || is_multisite() && $menu_perms['plugins'] ) {
+	$menu[65] = array( sprintf( __('Plugins %s'), "<span class='update-plugins count-$update_count'><span class='plugin-count'>" . number_format_i18n($update_count) . "</span></span>" ), 'activate_plugins', 'plugins.php', '', 'menu-top', 'menu-plugins', 'div' );
+		$submenu['plugins.php'][5]  = array( __('Installed'), 'activate_plugins', 'plugins.php' );
+		if ( is_super_admin() ) {
+			/* translators: add new plugin */
+			$submenu['plugins.php'][10] = array(_x('Add New', 'plugin'), 'install_plugins', 'plugin-install.php');
+		}
+		if ( !is_multisite() )
+			$submenu['plugins.php'][15] = array( __('Editor'), 'edit_plugins', 'plugin-editor.php' );
+}
 
 if ( current_user_can('edit_users') )
 	$menu[70] = array( __('Users'), 'edit_users', 'users.php', '', 'menu-top', 'menu-users', 'div' );
@@ -126,7 +129,11 @@
 if ( current_user_can('edit_users') ) {
 	$_wp_real_parent_file['profile.php'] = 'users.php'; // Back-compat for plugins adding submenus to profile.php.
 	$submenu['users.php'][5] = array(__('Authors &amp; Users'), 'edit_users', 'users.php');
-	$submenu['users.php'][10] = array(_x('Add New', 'user'), 'create_users', 'user-new.php');
+	if ( !is_multisite() )
+		$submenu['users.php'][10] = array(_x('Add New', 'user'), 'create_users', 'user-new.php');
+	elseif ( is_super_admin() || get_site_option( 'add_new_users' ) )
+		$submenu['users.php'][10] = array(__('Add New') . ' <strong>*</strong>', 'create_users', 'ms-options.php#addnewusers');
+		
 	$submenu['users.php'][15] = array(__('Your Profile'), 'read', 'profile.php');
 } else {
 	$_wp_real_parent_file['users.php'] = 'profile.php';
@@ -137,7 +144,8 @@
 	$submenu['tools.php'][5] = array( __('Tools'), 'read', 'tools.php' );
 	$submenu['tools.php'][10] = array( __('Import'), 'import', 'import.php' );
 	$submenu['tools.php'][15] = array( __('Export'), 'import', 'export.php' );
-	$submenu['tools.php'][20] = array( __('Upgrade'), 'install_plugins',  'update-core.php');
+	if ( is_super_admin() )
+		$submenu['tools.php'][20] = array( __('Upgrade'), 'install_plugins',  'update-core.php');
 
 $menu[80] = array( __('Settings'), 'manage_options', 'options-general.php', '', 'menu-top', 'menu-settings', 'div' );
 	$submenu['options-general.php'][10] = array(__('General'), 'manage_options', 'options-general.php');
@@ -147,7 +155,8 @@
 	$submenu['options-general.php'][30] = array(__('Media'), 'manage_options', 'options-media.php');
 	$submenu['options-general.php'][35] = array(__('Privacy'), 'manage_options', 'options-privacy.php');
 	$submenu['options-general.php'][40] = array(__('Permalinks'), 'manage_options', 'options-permalink.php');
-	$submenu['options-general.php'][45] = array(__('Miscellaneous'), 'manage_options', 'options-misc.php');
+	if ( is_super_admin() )
+		$submenu['options-general.php'][45] = array(__('Miscellaneous'), 'manage_options', 'options-misc.php');
 
 $_wp_last_utility_menu = 80; // The index of the last top-level menu in the utility menu group
 
Index: wp-admin/plugins.php
===================================================================
--- wp-admin/plugins.php	(revision 12614)
+++ wp-admin/plugins.php	(working copy)
@@ -236,6 +236,15 @@
 
 add_contextual_help('plugins', $help);
 
+if ( is_multisite() && is_super_admin() ) {
+	$menu_perms = get_site_option('menu_items', array());
+	if ( !$menu_perms['plugins'] ) {
+		$message = sprintf( __( 'The plugins page is not visible to normal users. It must be activated first. %s' ), '<a href="ms-options.php#menu">' . __( 'Activate' ) . '</a>' );
+		$message = str_replace( "'", "\'", "<div class='error'><p>$message</p></div>" );
+		add_action( 'admin_notices', create_function( '', "echo '$message';" ) );
+	}
+}
+
 $title = __('Manage Plugins');
 require_once('admin-header.php');