The work-flow of every application is managed by the file application/bootstrap.php. Here a simple example of how your bootstrap could looks like:
// include the Loader class
require_once LIBRARY_DIR . "Loader.php";
// init the loader
$loader = Loader::get_instance();
// init the database
$loader->init_db();
// load the controller selected with the URI
$loader->load_controller();
// draw the page
$loader->draw();
require_once LIBRARY_DIR . "Loader.php";
// init the loader
$loader = Loader::get_instance();
// init the database
$loader->init_db();
// load the controller selected with the URI
$loader->load_controller();
// draw the page
$loader->draw();