Jeffrey emailed a very detailed outline of what he thinks Cortana's captured AI might have been.
Jeffery Arnold (firstname.lastname@example.org) writes:
Just taking it back a little, back in First Strike we find out that the covenant have AIs. When John-117 put Cortana into the Covenant network on High Charity, Cortana mentions an unusually formidable presence, and eventually captures and contains the core coding of a covenant AI for further examination... However, the quick examination Cortana had done at the time had uncovered something that was very interesting, and yet to be answered...
The enemy AI code was so similar to Cortana, that Cortana says that it's as if it were her own code, only copied many times over, each time introducing subtle errors due to the replication process.
I believe it would be safe to assume, the "copied" AI Cortana captured was not the "unusually formidable presence" Cortana mentioned. This is due to the speed and ease Cortana had in capturing and stripping the "copied" AI. I would believe that the "unusually formidable presence" was more likely to be the originating code to the copied AI. Yet who would this originating AI be, that is so similar to Cortana in code?
Also of note in First Strike, the covenant scan the Halo Debris using Human frequencies, even though there was never before a mention of the Covenant doing such a thing in UNSC or ONI files. What would have caused the covenant to start this after the event of Halo: CE? Could it possible be due to the fact that the Covenant get their hands on a Human Smart AI after the events of Halo: CE?
But which AI would they have gotten? We only know of Cortana and Guilty Spark, and I doubt Guilty Sparks core coding looks anything like Cortana... Yet it couldn't have been Cortana, for she was with John the entire time... Except for when she went into the whole of the Halo system... Infiltrating every piece of it's infrastructure, being in all parts of it's network at once, including the parts the Covenant had access too...
What about Kalmiya, Cortana's "Older Sister"? She was apparently destroyed by Dr. Halsey using her fail-safe to terminate her so that the Covenant could not capture her, but what if this is not what truly happened? Kalmiya had known about her fail-safe after witnessing Dr. Halsey using Araquiel's to terminate Araquiel. And had even had the forethought to ask Dr. Halsey if she had one as well... She was a smart AI designed to test programing that eventually became Cortana, being a smart AI and Cortana's "Older Sister", it wouldn't be hard to assume that Kalmiya was already rampant and so stripped herself of her own fail-safe after seeing it used on Araquiel, only giving Dr. Halsey a "good show" when Dr. Halsey thought she had terminated Kalmiya. And thus when the Covenant infiltrated the base, and scoured it's systems, they would have found her. An AI with a rivalry for Cortana (the "better" her), with a core coding that would be almost exact, and the ability to adapt easily as her programing was made to do.
Kalmiya would make for quite an "unusually formidable presence" to Cortana... It would make for quite a good story.
On another note, this goes more with the Marathon connections... Whatever happened to Beowulf? Cortana had essentially done the same to him as she had done to the Covenant AI, right? What if, by the time Marathon takes place Cortana still exists, but is so rampant that she splits her consciousness to better stabilize herself? She would split into three, one part using her own coding (Leela), one part using the covenant AI coding (Tyco), and one using Beowulfs coding (Durandal). From the scene when Beowulf and Cortana exchange words, they seem to have a very similar relationship as Leela and Durandal, and the "Copy" AI would seem to fit the persona of Tyco... And being that Cortana has the ability to replicate herself, this wouldn't seem all that impossible. Halo might not be the predecessor of Marathon, but the predecessor of a re-imagined Marathon... Halo 3 ends with Master Chief and Cortana alone in a ship floating in dead space, with Cortana saying that it could take years for them to find anybody, and later(by possibly a few hundred years), they come to a planet (Tau Ceti anybody). Upon landing Master Chief would be conscripted into being a Security Officer for the ship in orbit, the Marathon, and Cortana (by this time already splitting into the three, not to Master Chiefs knowledge of course), would be moved aboard as it's Navigation, Life Support, and various Operations AI's.
I think the shift from one to the other would be quite easy to make, with slight changes in story from here to there... Being that everything Bungie is currently doing is pre-Halo 3 themed, I would feel that bungie is waiting for the right time to slam a new re-imagined set of Marathon games on us, a time when we're not expecting it (they have to get everything they can out of the halo stories first)... There obviously has to be something with that Halo 3 ending