There is Kira, Scott's new love interest and Allison is kinda in the way. Also aren't they about to kill Allison of something? I haven't watched this far, but this is what I heard. If she was still Scott's girlfriend it would have a much bigger impact. And I guess that she became Isaac's girlfriend so that there would be meer drama? Most people like love triangles.
After finding out that her aunt Kate was psychotic and a murderer and Allison's mother commits suicide rather than become a werewolf, Allison falls under the influence of her psychotic grandfather.
He tries to turn her into a cold-blooded killer (like he did what Kate) and in her grief, Allison lets him... When Gerard's TRUE plan is revealed, that he has cancer and wanted to get Derek in a position where he would have to bite him in order to cure the cancer. He planed to kill Derek once he transforms so that Gerard would be an Alpha and He threatens to have the Kanima kill Allison unless Scott helps him. Allison turns on him. Unable to cope with what she's done, Allison apologizes to Scott and breaks up with him.
Allison and her father leave Beacon Hills and spend four months living in France. While attempting to defeat the Alpha Pack, Isaac and Allison start to become attracted to each other. Their relationship develops in fits and starts and they spend in a single night together shortly before Allison's death.