Board Thread:General Discussion/@comment-79.52.61.188-20130415085048/@comment-1672596-20130709172618

Mr. Grave wrote: At this point, Zero's successor AIs could have began to create their own will. They probably didn't mind making an alliance with Cipher's archenemy when it suited them, and Big Boss planned to use this to his advantage. That's the only theory I can think of.

Yeah, except the AIs couldn't have been created until after 2000, due to the Y2K bug being a huge factor in the AI network's creation and especially the part about information control. MGS2 made that clear via Emma.