Not entirely what you are looking for, but this is the only one I can think of at the moment that matches your first request. It is an AU story in which Craig has Justin kidnapped by an organization that can fix him, and a worried Brian goes on a rescue mission to save him. It is Empty by ButterflyTiger_1982. Here is the link.
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timeasmymeasure
Brainwashing Story
Date: 2008-11-30 10:49 pm (UTC)http://www.midnightwhispers.ca/viewstory.php?sid=31