That's an interesting take on the plot. I still think there are enough hints in the game both from a plot point as well as a thematic perspective that lends itself to Cortana somehow becoming human.
Remember that "rampancy" is really considered a terminal disease and inevitable fate of all smart A.I.'s in the Halo universe. Resolving or curing it has been painted as impossible. Thus, it seems oversimplistic for Dr. Halsey to simply "flip a switch" or come up with a pat answer to just "fix" Cortana.
From my understanding of what rampancy is, a big part of it has to do with the A.I. reaching a level of sophistication where it understands what it truly is and the tragic implication that it can never become human no matter how "close" it can approximate that nature by more and more knowledge. Thus, insanity ensues.
In my opinion, the true "holy grail" of AI evolution is thus the unattainable goal of fully "becoming human."
In order to truly "cure" Cortana's rampancy, she must become human from her digital origin. Normally, this would of course be impossible. However, Cortana has a chance because she is not like other pure A.I. A part of real human tissue (from Halsey) was used in her creation. You can argue that to some extent Halsey is both Cortana and John's "mother."
In addition, we know that part of the Composer can do is to digitize human beings. The results were not good of course but as this technology exists, the implication must be considered that the reverse may also be possible. We still know very little about the true nature of the Didact and the Librarian and the ultimate role of both Master Chief and Cortana. We know already that the two of them (NOT JUST JOHN) are important for the future of the universe.
In the overall scheme of things, I think 343 wants to take a look at Master Chief and Cortana and decide what to do with that relationship. In terms of story telling, all good things must come to an end. Part of the definition of a good story is that it must have an ending, else it is incomplete. What then do we look forward to with the Halo epic as centered around Master Chief? Is it conceivable or even desirable to have him be spun out in endless sequels and adventures with Cortana as his constant guardian angel with her usual quips and sarcastic comments? Eventually, such a formula would grow stale and boring. We've already SEEN that relationship in the first Halo trilogy by Bungie and while it works fine in establishing the characters and relationship, we now want to see EVOLUTION.
I still think the endgame is to save Cortana's soul and mind and also grant her the impossible holy grail and dream of becoming human. Against the backdrop of your standard "save the universe" plot line with the Didact, i think it would be incredibly poetic and satisfying that you could also have something so personal and profound yet just as epic occur.
Saving Cortana should thus be just as difficult and just as epic as saving the universe since from John's point of view, the two may be almost equivalent. Indeed success in one may unwittingly be interwined with success in the other.
343 Studios have hinted that Halo 5 will be "darker" in tone. It's their "empire strikes back" middle chapter. In keeping with my instinct on how this story goes, I think it is increasingly likely that Cortana will be subverted by the Didact and become the primary villain in the next game. We certainly see small hints of possible temptation or corruption during Cortana's moments of ranting and raving during her rampancy. I don't think it's a stretch at all to think that she may be converted. There's certainly precedent for this in the Halo mythos with Mendicant Bias for example. We already see Master Chief disobey a direct order from Captain Del Rio to protect Cortana (which should come as a shock to those who understand John's background) and this is foreshadowing of the conflict that will be introduced when he will likely be ordered to destroy Cortana to save mankind. Will he? Can he?
Finally, in Halo 6, we will see Cortana's redemption at the hands of John and the ultimate resolution of the threat of the Didact. The issue of HUMANITY and what it truly means to be HUMAN appear to be a central theme in the Reclaimer trilogy. We have on the one hand a race (the Forerunners) who were willing to sacrifice their humanity and become "digital machines" to escape the Flood. Ironically, we have AI who are perfect digital creations who desperately wish to be human. Then we have humans like Master Chief who are more machine than man in their emotional state and how they deal with the world. I see a definite dichotomy and tension between the character of the Didact and Cortana and I think the ultimate resolution and eventual defeat of the Didact will be intertwined with Cortana achieving her final cure from rampancy by becoming human.
If this happens, then the reclaimer trilogy will end the adventures of Master Chief and Cortana. While the Halo universe will go on, this pair of heroes will get the rest they so richly deserve. As a fan of the CHARACTERS of Master Chief and Cortana, I want a better fate for them than endless war and battle. Master Chief's existence if you stop to really think about it is unspeakably sad and Cortana's fate no less tragic. I hope and I think 343 Studios is committed to telling us a story that will put these two beloved characters in a better place and ultimately that should involve Master Chief taking his armor off to become John and Cortana becoming human so they can stop fighting, start living, and also eventually die in peace. In this, the choice of Cortana reminds me of the lyrical beauty of Luthien and Arwen of the Elves in J.R.R. Tolkien's Lord of the Rings when they also made their choice to live as mortals with their loved ones and then pass on rather than the endless immortality of their brethren alone.
