I was sitting, thinking, when I had this kinda crazy thought, but it might prove to be a real twist(This does not mean that its a fact that Bungie is incorporating this into the plot...at least i hope not)
What if Cortana got incarnated into a real live body. My first thought was: Will she be hot? Don't know, but that would definitely be nice to have a hot chic in Halo 2. I wonder if she would be a good fighter? Would she command a ship? Would she continue to direct MC by radio? I think it would really be cool to actually "meet" Cortana, and see more of her. She's an interesting character, but she only shows up in the clips at the end of, or sometimes during, levels. Am I crazy, or do I just have Halo 2 fever. It was just an interesting thought.
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A more likely alternative to that would be to meet Dr. Halsey. She is the Dr. who took John 117 from his home and jump started the Spartan II program. Cortana is based off Dr. Halsey....and so they should look the same. And the chances of meeting up with her seem pretty good, because she sometimes supplies missions for John. Then again, she is off somewhere unkown with Kelly right now....