edit: found thanks to catnthecradle, The Usual Suspects Missing Scene http://www.livejournal.com/tools/memories.bml?user=catnthecradle&keyword=EP%3A2x07%3AThe%20Usual%20Suspects&filter=all

In the story I am looking for Dean was arrested, when he was being transferred to a different location he got raped. Sam and some other police officer show up just after Dean was raped. Sam finds out about what happened quite fast. They end up staying at the roadhouse while Dean is recovering because he was physically hurt. I remember that Ellen and Ash were trying to keep it a secret from Jo that Dean and Sam were staying at the roadhouse. Ellen made soup for Dean and stayed with him whenever he was eating, because he wasn't allowed to eat the same food as Sam.
I don't remember on what site it was hosted, or whether it was a WIP or finished.
Thanks in advance!