- last post: 01.01.0001 12:00 AM PDT
1) Her program has finally been corrupted by all the information she has absorbed and she is beginning to break down (read the books, A.I.s have a limited lifespan until they "think" themselves to death. This process is accelerated the more information that an A.I. absorbs).
2) She has been taken over by Gravemind, or she has joined sides with him, or she is just using him for some hidden purpose (learn more about Flood/Forerunners, get back to Master Chief, or transportation to the Ark).
Or a combination of the two
Personally, I believe she is going to use Gravemind to reach the Ark, kill him somehow or get Master Chief to kill him once she gets there, then take over the Ark and start the activation of the remaining Halo rings. Her motives will be to stop the Flood completely just like the Forerunners did, believing that there is no other way to beat them. Master Chief will stop/fight her somehow and she will regain her senses. Before fading away (because of her shortened lifespan) Cortana tearfully apologizes for betraying Master Chief and reveals that she can't stop the activation process. Cortana reveals that "there is only one other way..." and finally disentegrates from existance, as Master Chief calls out to her sorrowfully. Alone and faced with a decision to make, Master Chief remembers Dr. Hasley's final words before she disappeared with Kelly (read the books), "Your mission, John, is to save as many people as you can..." Master Chief finds some way to short-circuit or back-fire the Ark, sacrificing himself to destroy the Halo rings once and for all and save humanity...