I checked under the "b/j go to therapy" tag, but I didn't find this one; I'm not even completely certain it exists. (Is my imagination inventing it or combining other fics?)
In this fic, Justin is going to a psychiatrist/psychologist, perhaps right after the bashing. The shrink does a real number on Justin, screwing with his head, making him feel like everything that's gone wrong in his life is his own fault. The shrink may even be sexually abusing Justin. Brian doesn't realize what's going on at first as he's staying out of Justin's life (on Jennifer's orders?) but eventually comes to the rescue.
One detail I recall is Justin coming to see Brian and apologizing for complicating Brian's life. Brian notices that Justin has developed a new nervous habit (stroking the side of his own throat?) and decides to talk to Daphne on her impressions of how Justin is doing.
Update: It's
Vulnerable Points by
besame_bj. Thank you to
toto_too514 for the quick ID.