Zend Framework provides tools for creating PHP web applications. The zf script is used to generate a project skeleton and configure resources. The Zend_Application loads configuration from application.ini, initializes the bootstrap class, and runs the application. The bootstrap class initializes custom resources. Common resources like the front controller, database, and view are initialized through Zend_Application_Resource classes, which get configuration options from application.ini. This allows flexible configuration and initialization of an MVC application in Zend Framework.