I think that she is possessed by the Nogitsune, or at least the same one that is 'controlling' Stiles. It has been said one to many times "Kitsunes are trickster spirits." While Stiles is made to be seen as the big bad, and all the attention is focused on him, Nogitsune!Allison is working quietly behind the scenes, getting rid of everyone who could get in her way, especially Chris Argent and Derek Hale, whom were not only arrested, but nearly killed.
What if the Nogitsune is jumping between bodies, using Stiles to keep the attention off of Allison. What has Allison been doing this season? Sleeping with her phone turned off (which apparently is unusual for her), dreaming about her dead aunt, killing Isaac in bed. I think that she took the emitter from her father (which wouldn't be difficult considering she has gotten guns, knives, crossbows, and other devices from there before) and put it in Derek's loft to lure him to the Argent home, where they would later be arrested and taken to the Police center where they would be blown up.
Isn't it also suspiscious that she was the only character that wasn't checked by the Oni? Even Silverfinger (Katashi, the Yakuza dude) told Chris to kill her if she was possessed by the Kitsune. So she killed him and framed her father, getting rid of both of them.
Worst part, I think that she'll be the one to die. She'll be the one to make Scott finally realize that he needs to start upping his game. What would do that better than killing his (mostly likely) first ex-girlfriend? This might even drive him to creating his own pack or even giving him the ability to get his own Alpha form/Full Shift. This would also have an effect on Chris. Maybe losing his entire family would finally get him to realize that werewolves are not the problem and that he should be helping Derek and Scott protect the town. Killing Stiles would not only be the worst thing for the show considering everyone loves him. Killing Derek is going back on his 'teaching you some tools of the trade' business (plus Jeff Davis would be burned at the stake for killing any chance of Sterek by the Sterek shippers.) Kira is too new and too unexplored as a character to be killed, plus she is the new creature and new love interest this season. Lydia still hasn't gotten a full disclosure on her abilties and has already been confirmed for next season. Peter will most likely be the next big bad for season 4, so thats not possible.