Does the functions.php file ever get called during an AJAX call? Debug AJAX

Trying to figure out an issue a fellow programmer is having. I was wondering if the functions.php file get called at all when you do admin side AJAX? I know that when you do an AJAX call a part of WP gets loaded up to process the call and send back a response. Is the functions.php file included in that?

The reason I’m asking is because he’s using the class from the Meta-Box` plugin and loading it as part of a theme instead. There is some AJAX in that class that only returns empty responses and I think its because the code that handles the response doesn’t get loaded. Is there any documentation to what gets loaded when WP handles AJAX?