If your looking at code, all the hook_menu function calls is how the non alias paths get created. Things like users and nodes use a % in the path creation; this turns into the argument for the page callback function. Read more about this here: Wildcard Loader Arguments.
node_menu()
function node_menu() {
...
$items['node/%node'] = array(
'title callback' => 'node_page_title',
'title arguments' => array(1),
'page callback' => 'node_page_view',
'page arguments' => array(1),
'access callback' => 'node_access',
'access arguments' => array('view', 1),
'type' => MENU_CALLBACK,
);
...
}
user_menu()
function user_menu() {
...
$items['user/%user_uid_optional'] = array(
'title' => 'My account',
'title callback' => 'user_page_title',
'title arguments' => array(1),
'page callback' => 'user_view',
'page arguments' => array(1),
'access callback' => 'user_view_access',
'access arguments' => array(1),
'parent' => '',
'file' => 'user.pages.inc',
);
...
}
The function that handles this menu information is menu_execute_active_handler().
Aliases happen as the 2nd to last part of the bootstrap in the drupal_init_path function. It converts /about-us into node/4 for internal use.
For more in depth information check out this link: Drupal menu system (Drupal 6.x)