Okay so I've been trying and utterly failing at my google skills to find this fic for the past couple hours...
In the fic Jared and Tom started dating and Jensen was really protective of Jared, he didn't want him involved with Tom at all.
Tom became abusive (starting with emotional abuse then to sexual and physical) and Jensen helped Jared to leave.
I think there was a sequel to this also.
Hope someone can help!