Index: wp-admin/includes/plugin.php
===================================================================
--- wp-admin/includes/plugin.php	(revision 12932)
+++ wp-admin/includes/plugin.php	(working copy)
@@ -259,7 +259,7 @@
  * @return bool True, if in the active plugins list. False, not in the list.
  */
 function is_plugin_active( $plugin ) {
-	return in_array( $plugin, apply_filters( 'active_plugins', get_option( 'active_plugins', array() ) ) );
+	return in_array( $plugin, (array) get_option( 'active_plugins', array() ) ) || is_plugin_active_for_network( $plugin );
 }
 
 /**
@@ -270,7 +270,7 @@
  * @param string $plugin Base plugin path from plugins directory.
  * @return bool True, if active for the network, otherwise false.
  */
-function is_plugin_active_for_network( $plugin ){
+function is_plugin_active_for_network( $plugin ) {
 	if ( !is_multisite() )
 		return false;
 
@@ -553,7 +553,7 @@
  * @return array invalid plugins, plugin as key, error as value
  */
 function validate_active_plugins() {
-	$plugins = apply_filters( 'active_plugins', get_option( 'active_plugins', array() ) );
+	$plugins = get_option( 'active_plugins', array() );
 	// validate vartype: array
 	if ( ! is_array( $plugins ) ) {
 		update_option( 'active_plugins', array() );
@@ -562,7 +562,7 @@
 
 	if ( is_multisite() && is_super_admin() ) {
 		$network_plugins = (array) get_site_option( 'active_sitewide_plugins', array() );
-		$plugins = array_merge( (array) $plugins, $network_plugins );
+		$plugins = array_merge( $plugins, $network_plugins );
 	}
 
 	if ( empty( $plugins ) )
Index: wp-admin/includes/upgrade.php
===================================================================
--- wp-admin/includes/upgrade.php	(revision 12932)
+++ wp-admin/includes/upgrade.php	(working copy)
@@ -1074,6 +1074,7 @@
  * @since 3.0.0
  */
 function upgrade_network() {
+	global $wp_current_db_version;
 	// 2.8
 	if ( $wp_current_db_version < 11549 ) {
 		$wpmu_sitewide_plugins = get_site_option( 'wpmu_sitewide_plugins' );
@@ -1086,8 +1087,8 @@
 
 			update_site_option( 'active_sitewide_plugins', $sitewide_plugins );
 		}
-		update_site_option( 'wpmu_sitewide_plugins', '' );
-		update_site_option( 'deactivated_sitewide_plugins', '' );
+		delete_site_option( 'wpmu_sitewide_plugins' );
+		delete_site_option( 'deactivated_sitewide_plugins' );
 	}
 }
 
Index: wp-includes/load.php
===================================================================
--- wp-includes/load.php	(revision 12932)
+++ wp-includes/load.php	(working copy)
@@ -403,13 +403,8 @@
  */
 function wp_load_plugins() {
 	$plugins = array();
+	$active_plugins = (array) get_option( 'active_plugins', array() );
 
-	// Check for hacks file if the option is enabled
-	if ( get_option( 'hack_file' ) && file_exists( ABSPATH . 'my-hacks.php' ) )
-			$plugins[] = ABSPATH . 'my-hacks.php';
-
-	$active_plugins = (array) apply_filters( 'active_plugins', get_option( 'active_plugins', array() ) );
-
 	// Get active network plugins
 	if ( is_multisite() ) {
 		$active_sitewide_plugins = (array) get_site_option( 'active_sitewide_plugins', array() );
@@ -419,6 +414,12 @@
 		}
 	}
 
+	// Check for hacks file if the option is enabled
+	if ( get_option( 'hack_file' ) && file_exists( ABSPATH . 'my-hacks.php' ) ) {
+		_deprecated_file( 'my-hacks.php', '1.5' );
+		array_unshift( $plugins, ABSPATH . 'my-hacks.php' );
+	}
+
 	if ( empty( $active_plugins ) || defined( 'WP_INSTALLING' ) )
 		return $plugins;