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So yeah, in this AU Billy and Peter had something between them (Billy is one of Peter's six roomates at the conservatory) but neither of them wanted to make it formal. Even though Billy said he had no problem really and had nothing against him being with Jess (since he knew it was just to avoid suspicions from their fraternity partners and the sorority girls) He did call the sorority house to disturb Jess and the others to such an extent that he and Peter had a fight after the latter found out that Billy had been doing this for months, telling him that this could raise suspicions (this fight was a few days before Christmas and what happened in the movie) When Peter went to talk to Jess about his plans, there he meets Billy in the sorority house, tells him about what happened at his piano concert and how he plans to solve everything. That’s how Billy finds out that Peter wants to marry Jess and that she is pregnant (but not that she doesn’t want have the baby or marry Peter, he’ll heard their conversation later). 

When Peter's plan does not go as he wants, they both come together to finish what Billy started, of course neither of them expected that Jess could kill Peter when he chased her down to the basement.