diff --git a/assets/js/plugin-check-admin.js b/assets/js/plugin-check-admin.js
index 22ac0bdd1..9c2a3f13f 100644
--- a/assets/js/plugin-check-admin.js
+++ b/assets/js/plugin-check-admin.js
@@ -12,7 +12,9 @@
 		e.preventDefault();
 
 		getChecksToRun()
+		.then( setUpEnvironment )
 		.then( runChecks )
+		.then( cleanUpEnvironment )
 		.then(
 			( data ) => {
 				console.log( data.message );
@@ -25,17 +27,95 @@
 		);
 	} );
 
+	/**
+	 * Setup the runtime environment if needed.
+	 *
+	 * @since n.e.x.t
+	 */
+	function setUpEnvironment( data ) {
+		const pluginCheckData = new FormData();
+		pluginCheckData.append( 'nonce', pluginCheck.nonce );
+		pluginCheckData.append( 'plugin', data.plugin );
+		pluginCheckData.append( 'action', 'plugin_check_set_up_environment' );
+
+		for (var i = 0; i < data.checks.length; i++) {
+			pluginCheckData.append( 'checks[]', data.checks[ i ] );
+		}
+
+		return fetch(
+			ajaxurl,
+			{
+				method: 'POST',
+				credentials: 'same-origin',
+				body: pluginCheckData
+			}
+		)
+		.then(
+			( response ) => {
+				return response.json();
+			}
+		)
+		.then( handleDataErrors )
+		.then(
+			( data ) => {
+				if ( ! data.data || ! data.data.message ) {
+					throw new Error( 'Response contains no data.' );
+				}
+
+				console.log( data.data.message );
+
+				return data.data;
+			}
+		);
+	}
+
+	/**
+	 * Cleanup the runtime environment.
+	 *
+	 * @since n.e.x.t
+	 */
+	function cleanUpEnvironment( data ) {
+		const pluginCheckData = new FormData();
+		pluginCheckData.append( 'nonce', pluginCheck.nonce );
+		pluginCheckData.append( 'action', 'plugin_check_clean_up_environment' );
+
+		return fetch(
+			ajaxurl,
+			{
+				method: 'POST',
+				credentials: 'same-origin',
+				body: pluginCheckData
+			}
+		)
+		.then(
+			( response ) => {
+				return response.json();
+			}
+		)
+		.then( handleDataErrors )
+		.then(
+			( data ) => {
+				if ( ! data.data || ! data.data.message ) {
+					throw new Error( 'Response contains no data.' );
+				}
+
+				console.log( data.data.message );
+
+				return data.data;
+			}
+		);
+	}
+
+
 	/**
 	 * Get the Checks to run.
 	 *
 	 * @since n.e.x.t
 	 */
 	function getChecksToRun() {
-		// Collect the data to pass along for generating a check results.
 		const pluginCheckData = new FormData();
 		pluginCheckData.append( 'nonce', pluginCheck.nonce );
 		pluginCheckData.append( 'plugin', pluginsList.value );
-		pluginCheckData.append( 'checks', [] );
 		pluginCheckData.append( 'action', 'plugin_check_get_checks_to_run' );
 
 		return fetch(
@@ -73,9 +153,12 @@
 		const pluginCheckData = new FormData();
 		pluginCheckData.append( 'nonce', pluginCheck.nonce );
 		pluginCheckData.append( 'plugin', data.plugin );
-		pluginCheckData.append( 'checks', data.checks );
 		pluginCheckData.append( 'action', 'plugin_check_run_checks' );
 
+		for (var i = 0; i < data.checks.length; i++) {
+			pluginCheckData.append( 'checks[]', data.checks[ i ] );
+		}
+
 		return fetch(
 			ajaxurl,
 			{
diff --git a/includes/Admin/Admin_AJAX.php b/includes/Admin/Admin_AJAX.php
index a9b537ab8..1299c6973 100644
--- a/includes/Admin/Admin_AJAX.php
+++ b/includes/Admin/Admin_AJAX.php
@@ -11,7 +11,9 @@
 use Exception;
 use WordPress\Plugin_Check\Checker\AJAX_Runner;
 use WordPress\Plugin_Check\Checker\Runtime_Check;
+use WordPress\Plugin_Check\Checker\Runtime_Environment_Setup;
 use WordPress\Plugin_Check\Utilities\Plugin_Request_Utility;
+
 /**
  * Class to handle the Admin AJAX requests.
  *
@@ -33,6 +35,8 @@ class Admin_AJAX {
 	 * @since n.e.x.t
 	 */
 	public function add_hooks() {
+		add_action( 'wp_ajax_plugin_check_clean_up_environment', array( $this, 'clean_up_environment' ) );
+		add_action( 'wp_ajax_plugin_check_set_up_environment', array( $this, 'set_up_environment' ) );
 		add_action( 'wp_ajax_plugin_check_get_checks_to_run', array( $this, 'get_checks_to_run' ) );
 		add_action( 'wp_ajax_plugin_check_run_checks', array( $this, 'run_checks' ) );
 	}
@@ -46,6 +50,100 @@ public function get_nonce() {
 		return wp_create_nonce( self::NONCE_KEY );
 	}
 
+	/**
+	 * Handles the AJAX request to setup the runtime environment if needed.
+	 *
+	 * @since n.e.x.t
+	 */
+	public function set_up_environment() {
+		// Verify the nonce before continuing.
+		$valid_nonce = $this->verify_nonce( filter_input( INPUT_POST, 'nonce', FILTER_SANITIZE_STRING ) );
+
+		if ( is_wp_error( $valid_nonce ) ) {
+			wp_send_json_error( $valid_nonce, 403 );
+		}
+		$runner = Plugin_Request_Utility::get_runner();
+
+		if ( is_null( $runner ) ) {
+			$runner = new AJAX_Runner();
+		}
+
+		// Make sure we are using the correct runner instance.
+		if ( ! ( $runner instanceof AJAX_Runner ) ) {
+			wp_send_json_error(
+				new WP_Error( 'invalid-runner', __( 'AJAX Runner was not initialized correctly.', 'plugin-check' ) ),
+				500
+			);
+		}
+
+		$checks = filter_input( INPUT_POST, 'checks', FILTER_DEFAULT, FILTER_FORCE_ARRAY );
+		$plugin = filter_input( INPUT_POST, 'plugin', FILTER_SANITIZE_STRING );
+
+		try {
+			$runner->set_check_slugs( $checks );
+			$runner->set_plugin( $plugin );
+			$checks_to_run = $runner->get_checks_to_run();
+		} catch ( Exception $error ) {
+			wp_send_json_error(
+				new WP_Error( 'invalid-request', $error->getMessage() ),
+				400
+			);
+		}
+
+		$message = __( 'No runtime checks, runtime environment was not setup.', 'plugin-check' );
+
+		if ( $this->has_runtime_check( $checks_to_run ) ) {
+			$runtime = new Runtime_Environment_Setup();
+			$runtime->setup();
+			$message = __( 'Runtime environment setup successful.', 'plugin-check' );
+		}
+
+		wp_send_json_success(
+			array(
+				'message' => $message,
+				'plugin'  => $plugin,
+				'checks'  => $checks,
+			)
+		);
+	}
+
+	/**
+	 * Handles the AJAX request to cleanup the runtime environment.
+	 *
+	 * @since n.e.x.t
+	 */
+	public function clean_up_environment() {
+		global $wpdb;
+
+		// Verify the nonce before continuing.
+		$valid_nonce = $this->verify_nonce( filter_input( INPUT_POST, 'nonce', FILTER_SANITIZE_STRING ) );
+
+		if ( is_wp_error( $valid_nonce ) ) {
+			wp_send_json_error( $valid_nonce, 403 );
+		}
+
+		// Set the new prefix.
+		$old_prefix = $wpdb->set_prefix( 'wppc_' );
+
+		$message = __( 'Runtime environment was not prepared, cleanup was not run.', 'plugin-check' );
+
+		// Test if the runtime environment tables exist.
+		if ( 'wppc_posts' === $wpdb->get_var( "SHOW TABLES LIKE 'wppc_posts'" ) || defined( 'WP_PLUGIN_CHECK_OBJECT_CACHE_DROPIN_VERSION' ) ) {
+			$runtime = new Runtime_Environment_Setup();
+			$runtime->cleanup();
+			$message = __( 'Runtime environment cleanup successful.', 'plugin-check' );
+		}
+
+		// Restore the old prefix.
+		$wpdb->set_prefix( $old_prefix );
+
+		wp_send_json_success(
+			array(
+				'message' => $message,
+			)
+		);
+	}
+
 	/**
 	 * Handles the AJAX request that returns the checks to run.
 	 *
@@ -59,9 +157,9 @@ public function get_checks_to_run() {
 			wp_send_json_error( $valid_nonce, 403 );
 		}
 
-		$checks = filter_input( INPUT_POST, 'checks', FILTER_DEFAULT, FILTER_REQUIRE_ARRAY );
+		$checks = filter_input( INPUT_POST, 'checks', FILTER_DEFAULT, FILTER_FORCE_ARRAY );
+		$checks = is_null( $checks ) ? array() : $checks;
 		$plugin = filter_input( INPUT_POST, 'plugin', FILTER_SANITIZE_STRING );
-
 		$runner = Plugin_Request_Utility::get_runner();
 
 		if ( is_null( $runner ) ) {
diff --git a/includes/Checker/AJAX_Runner.php b/includes/Checker/AJAX_Runner.php
index 77409b324..7ebd3b8fe 100644
--- a/includes/Checker/AJAX_Runner.php
+++ b/includes/Checker/AJAX_Runner.php
@@ -70,13 +70,6 @@ protected function get_plugin_param() {
 	 * @return array An array of Check slugs to run.
 	 */
 	protected function get_check_slugs_param() {
-		$checks = array();
-
-		if ( isset( $_REQUEST['checks'] ) ) {
-			// Checks are passed as a comma separated string.
-			$checks = wp_parse_list( $_REQUEST['checks'] );
-		}
-
-		return $checks;
+		return filter_input( INPUT_POST, 'checks', FILTER_DEFAULT, FILTER_FORCE_ARRAY );
 	}
 }
diff --git a/includes/Checker/Abstract_Check_Runner.php b/includes/Checker/Abstract_Check_Runner.php
index d2b46c662..6c9cea18c 100644
--- a/includes/Checker/Abstract_Check_Runner.php
+++ b/includes/Checker/Abstract_Check_Runner.php
@@ -195,12 +195,12 @@ public function run() {
 	}
 
 	/**
-	 * Determines if any of the checks contains at least one runtime check.
+	 * Determines if any of the checks are a runtime check.
 	 *
 	 * @since n.e.x.t
 	 *
 	 * @param array $checks An array of check instances to run.
-	 * @return bool Returns true if one or more checks contains at least one runtime check.
+	 * @return bool Returns true if one or more checks is a runtime check.
 	 */
 	protected function has_runtime_check( array $checks ) {
 		foreach ( $checks as $check ) {
diff --git a/includes/Checker/Preparations/Force_Single_Plugin_Preparation.php b/includes/Checker/Preparations/Force_Single_Plugin_Preparation.php
index 5041b283d..dbc50fc5d 100644
--- a/includes/Checker/Preparations/Force_Single_Plugin_Preparation.php
+++ b/includes/Checker/Preparations/Force_Single_Plugin_Preparation.php
@@ -82,7 +82,14 @@ public function prepare() {
 	public function filter_active_plugins( $active_plugins ) {
 		if ( is_array( $active_plugins ) && in_array( $this->plugin_basename, $active_plugins, true ) ) {
 
-			$plugin_base_file = plugin_basename( WP_PLUGIN_CHECK_MAIN_FILE );
+			if ( defined( 'WP_PLUGIN_CHECK_MAIN_FILE' ) ) {
+				$plugin_check_file = WP_PLUGIN_CHECK_MAIN_FILE;
+			} else {
+				$plugins_dir       = defined( 'WP_PLUGIN_DIR' ) ? WP_PLUGIN_DIR : WP_CONTENT_DIR . '/plugins';
+				$plugin_check_file = $plugins_dir . '/plugin-check/plugin-check.php';
+			}
+
+			$plugin_base_file = plugin_basename( $plugin_check_file );
 
 			// If the plugin-check is the only available plugin then return that one only.
 			if ( $this->plugin_basename === $plugin_base_file ) {
diff --git a/includes/Checker/Preparations/Universal_Runtime_Preparation.php b/includes/Checker/Preparations/Universal_Runtime_Preparation.php
index cd4ab8793..633cc93fd 100644
--- a/includes/Checker/Preparations/Universal_Runtime_Preparation.php
+++ b/includes/Checker/Preparations/Universal_Runtime_Preparation.php
@@ -54,7 +54,14 @@ public function prepare() {
 
 		$cleanup_functions = array();
 
-		$use_minimal_theme_preparation = new Use_Minimal_Theme_Preparation( 'wp-empty-theme', WP_PLUGIN_CHECK_PLUGIN_DIR_PATH . '/test-content/themes' );
+		if ( ! defined( 'WP_PLUGIN_CHECK_PLUGIN_DIR_PATH' ) ) {
+			$plugins_dir  = defined( 'WP_PLUGIN_DIR' ) ? WP_PLUGIN_DIR : WP_CONTENT_DIR . '/plugins';
+			$theme_folder = $plugins_dir . '/plugin-check/test-content/themes';
+		} else {
+			$theme_folder = WP_PLUGIN_CHECK_PLUGIN_DIR_PATH . 'test-content/themes';
+		}
+
+		$use_minimal_theme_preparation = new Use_Minimal_Theme_Preparation( 'wp-empty-theme', $theme_folder );
 		$cleanup_functions[]           = $use_minimal_theme_preparation->prepare();
 
 		$force_single_plugin_preparation = new Force_Single_Plugin_Preparation( $this->check_context->basename() );
diff --git a/includes/Utilities/Plugin_Request_Utility.php b/includes/Utilities/Plugin_Request_Utility.php
index 0949f27ff..06c4f04a3 100644
--- a/includes/Utilities/Plugin_Request_Utility.php
+++ b/includes/Utilities/Plugin_Request_Utility.php
@@ -93,9 +93,14 @@ public static function initialize_runner() {
 
 		foreach ( $runners as $runner ) {
 			if ( $runner->is_plugin_check() ) {
-				// @TODO: Handle the cleanup function in later issue with shutdown action or method that returns cleanup functions.
-				static::$cleanup = $runner->prepare();
-				static::$runner  = $runner;
+				add_action(
+					'muplugins_loaded',
+					function() use ( $runner ) {
+						static::$cleanup = $runner->prepare();
+						static::$runner  = $runner;
+					}
+				);
+
 				break;
 			}
 		}
diff --git a/tests/Checker/AJAX_Runner_Tests.php b/tests/Checker/AJAX_Runner_Tests.php
index 4e4f75bb9..f4bd41bcb 100644
--- a/tests/Checker/AJAX_Runner_Tests.php
+++ b/tests/Checker/AJAX_Runner_Tests.php
@@ -52,7 +52,7 @@ public function test_prepare_with_runtime_check() {
 		add_filter( 'wp_doing_ajax', '__return_true' );
 		$_REQUEST['action'] = 'plugin_check_run_checks';
 		$_REQUEST['plugin'] = 'plugin-check';
-		$_REQUEST['checks'] = 'runtime_check';
+		$_REQUEST['checks'] = array( 'runtime_check' );
 
 		add_filter(
 			'wp_plugin_check_checks',
@@ -89,7 +89,7 @@ public function test_prepare_with_static_check() {
 		add_filter( 'wp_doing_ajax', '__return_true' );
 		$_REQUEST['action'] = 'plugin_check_run_checks';
 		$_REQUEST['plugin'] = 'plugin-check';
-		$_REQUEST['checks'] = 'empty_check';
+		$_REQUEST['checks'] = array( 'empty_check' );
 
 		add_filter(
 			'wp_plugin_check_checks',
@@ -121,7 +121,7 @@ public function test_run() {
 		add_filter( 'wp_doing_ajax', '__return_true' );
 		$_REQUEST['action'] = 'plugin_check_run_checks';
 		$_REQUEST['plugin'] = 'plugin-check';
-		$_REQUEST['checks'] = 'empty_check';
+		$_REQUEST['checks'] = array( 'empty_check' );
 
 		add_filter(
 			'wp_plugin_check_checks',
@@ -145,7 +145,7 @@ public function test_run_with_errors() {
 		add_filter( 'wp_doing_ajax', '__return_true' );
 		$_REQUEST['action'] = 'plugin_check_run_checks';
 		$_REQUEST['plugin'] = 'plugin-check';
-		$_REQUEST['checks'] = 'error_check';
+		$_REQUEST['checks'] = array( 'error_check' );
 
 		add_filter(
 			'wp_plugin_check_checks',
@@ -174,7 +174,7 @@ public function test_runner_initialized_early_throws_plugin_basename_exception()
 		add_filter( 'wp_doing_ajax', '__return_true' );
 		$_REQUEST['action'] = 'plugin_check_run_checks';
 		$_REQUEST['plugin'] = 'plugin-check';
-		$_REQUEST['checks'] = 'empty_check';
+		$_REQUEST['checks'] = array( 'empty_check' );
 
 		$muplugins_loaded = $wp_actions['muplugins_loaded'];
 		unset( $wp_actions['muplugins_loaded'] );
@@ -198,7 +198,7 @@ public function test_runner_initialized_early_throws_checks_exception() {
 		add_filter( 'wp_doing_ajax', '__return_true' );
 		$_REQUEST['action'] = 'plugin_check_run_checks';
 		$_REQUEST['plugin'] = 'plugin-check';
-		$_REQUEST['checks'] = 'empty_check';
+		$_REQUEST['checks'] = array( 'empty_check' );
 
 		$muplugins_loaded = $wp_actions['muplugins_loaded'];
 		unset( $wp_actions['muplugins_loaded'] );
diff --git a/tests/Utilities/Plugin_Request_Utility_Tests.php b/tests/Utilities/Plugin_Request_Utility_Tests.php
index c790a4d38..6ef368959 100644
--- a/tests/Utilities/Plugin_Request_Utility_Tests.php
+++ b/tests/Utilities/Plugin_Request_Utility_Tests.php
@@ -47,6 +47,9 @@ public function test_initialize_runner_with_cli() {
 		);
 
 		Plugin_Request_Utility::initialize_runner();
+
+		do_action( 'muplugins_loaded' );
+
 		$runner = Plugin_Request_Utility::get_runner();
 
 		unset( $_SERVER['argv'] );
@@ -60,6 +63,9 @@ public function test_initialize_runner_with_ajax() {
 		$_REQUEST['plugin'] = 'plugin-check';
 
 		Plugin_Request_Utility::initialize_runner();
+
+		do_action( 'muplugins_loaded' );
+
 		$runner = Plugin_Request_Utility::get_runner();
 
 		$this->assertInstanceOf( AJAX_Runner::class, $runner );
@@ -90,6 +96,8 @@ function( $checks ) {
 
 		Plugin_Request_Utility::initialize_runner();
 
+		do_action( 'muplugins_loaded' );
+
 		// Determine if one of the Universal_Runtume_Preparation was run.
 		$prepared = has_filter( 'option_active_plugins' );
 
@@ -114,7 +122,7 @@ public function test_destroy_runner_with_ajax() {
 		add_filter( 'wp_doing_ajax', '__return_true' );
 		$_REQUEST['action'] = 'plugin_check_run_checks';
 		$_REQUEST['plugin'] = 'plugin-check';
-		$_REQUEST['checks'] = 'runtime_check';
+		$_REQUEST['checks'] = array( 'runtime_check' );
 
 		add_filter(
 			'wp_plugin_check_checks',
@@ -130,6 +138,8 @@ function( $checks ) {
 
 		Plugin_Request_Utility::initialize_runner();
 
+		do_action( 'muplugins_loaded' );
+
 		// Determine if one of the Universal_Runtume_Preparation was run.
 		$prepared = has_filter( 'option_active_plugins' );