DISCLAIMER: I don't own Halo; that belongs to Bungie, Microsoft, and other people.
SUMMARY: What ultimately happened to the Master Chief and Cortana? Here's one out-there theory…
SPOILERS: Well, I'd say the entire Halo trilogy proper would be useful, especially given the details from the Terminals in Halo 3 and the story which they tell about the Forerunners against
the Flood, namely the Forerunner lovers Didact and Librarian. Oh, and this also makes reference to Cortana's tale in the 2-part "Origins" shorts from Halo Legends.
RATING: Doesn't really go into the detail or the gritty stuff of the Halo universe itself, but I figure I might just rate it "T" or "PG-13", just to be safe.
AUTHOR'S NOTES: This is based on a personal theory and crazy idea of mine… after looking at two particular pairs of characters in the Halo universe (Master Chief and Cortana, Didact and Librarian).

"Past, Present, and Future"

By Quillian

Dedicated with much thanks to nealtron5000, my loyal beta-reader.

I would also like to thank the YouTube user Vicks007kid for his Halo 3 walkthroughs which allowed me to see how the story ends (given how I don't have my own copy of the game, let alone any kind of XBox).

Living in the past is a luxury none of us can afford. We must learn from it, but we cannot live there. It is impossible to plan for the now – the present is ever fleeting. The future is where we must live. The future is what we must plan for.

–Excerpt from 24 terrabyte data image extracted from Forerunner Terminal Network

It's so beautiful here… the only thing missing is you.

I have lived for a very long time, across ages, much longer than an AI like me would have been expected to live – at least by her human creators – and I have managed to enjoy and indulge in the full spectrum of human emotions… but now, the feel of loneliness and sadness has become more intense than ever before.

For how can I feel any differently when I think about you, my dear Didact… or, should I say, John?

That is how I feel, as the Librarian… but better and originally known as Cortana.

You, Master Chief Petty Officer of the Navy, John-117, SPARTAN-II Commando of the UNSC Naval Special Warfare Command, and me, UNSC Artificial Intelligence serial number CTN 0452-9, nicknamed "Cortana"… then to become "Didact" and "Librarian" among the Forerunners themselves.

But as for how that happened…

As we were fleeing the Ark and heading back through the Portal to Earth, we got caught between the blast from the incomplete and unstable Installation 04b behind us and the Portal collapsing in front of us. Afterwards, we ended up drifting through space, and you went into sleep in a cryotube and I watched over you.

I tried to find ways to pass the time as we drifted endlessly through space, and as I slowly yet inevitably fell into rampancy, I recounted the known history of the galaxy from the time of the Forerunners to our present… even if it wasn't entirely accurate and I tried to fill in some of the blanks with more details. Anything to try to avoid thinking about rampancy, my own personal demise.

However, soon enough, it became clear that we had not just drifted through space… but had gone through time as well.

This had become quite apparent once you were revived from your cold slumber, and you found yourself face-to-face with the Forerunners themselves. They found you, a never-before-seen alien being, with a borderline rampant AI in tow.

It didn't take long for you to recognize them for who they were; even if you had never seen them before to know what they looked like, you immediately recognized them from their architecture and their technology.

However, at the same time, they were puzzled by you too. They had encompassed the length and breadth of this great galaxy, and they had never seen an alien being quite like you before.

There was not much time for long, drawn-out moments of shock and awe, as both you and they were aware of me, now descending into irreversible rampancy… that is, unless something could be done about that, to save me from rampancy.

Fortunately, they had a solution: For because they had Artificial Intelligence programs of their own, they knew of ways to extend my own "life expectancy." Once they plugged me into one of their machines, they were able to sort me out and fix me, and extend my life indefinitely.

But more than me, they were more surprised at you: An alien the likes of which they had never seen before, obviously built for combat, and along with weapons in a warship which was sheared in half.

Oh, you did your best to keep a low profile, despite the unbelievable and unprecedented circumstances; you played dumb just long enough to learn more about these new aliens, and from that, we were able to deduce that they were the Forerunners themselves.

They were quite hospitable towards the both of us; had more records of them existed in our time, then perhaps they would have also been known for their hospitality as well as their great feats of astrophysical engineering.

You tried not to give too much away, but eventually, it all came out (or at least the pertinent parts of it): You were from the future, a time when the human race was under attack from the alien Covenant, and both factions in that senseless war had stumbled upon Halo and the Flood. At first, both you and I agreed that perhaps it was not best to tell them of future events for fear of altering the course of history itself, but all too soon it became inevitable, and we had to tell them in order to convince them of our sincerity and good intentions. Fortunately, the Forerunner leadership could be trusted with your highly sensitive and important information, and so they convinced the rest of their people to accept you, even trust you.

And it all turned out to be rather convenient timing… because the first reports had come back from a world known as G 617 g about an alien and dangerous life form.

It was the Flood.

You were certainly a warrior for the ages, Master Chief, because almost no sooner than had you finished one fight against a formidable alien enemy than did you begin to engage yet another. And once again, Chief, I was at your side.

However, in order to truly assimilate with the Forerunners, you and I also had to take on new aliases… particularly as not to let future civilizations know that we had gone back in time.

You taught the Forerunners, a people who had long since put aside their internal differences and united into a peaceful people who had not known war for several generations, how to fight once again, especially this new foe, the Flood. Meanwhile, I took on a significant role in aiding and assisting with the preservation of knowledge, cataloguing everything I could to survive the war against the Flood and even beyond that.

We took on these names relevant to our roles: You were the Didact, and I was the Librarian.

For three hundred years, the Forerunner-Flood War raged on. That may seem like an incredibly and impossibly long time for a person to be alive and fighting – well, to another normal human, at least – but then again, you had long since ceased being a normal human. The humans of our time had average life expectancies of one hundred years or more, and with the biological enhancements of the Spartan project, you could now live well beyond that. Combine that with the generous care which the Forerunners had given you upon your arrival, and… well, who knows how long you could have lived for otherwise.

You were the greatest warrior of them all, Chief and Didact, leading the others into battle and teaching them through combat on the battlefield itself. Who better to teach them than the hero who almost singlehandedly turned the tide of the human war against the Covenant and eventually win the war against them?

That sadly misguided theocratic conglomerate known as the Covenant was one thing… however, the relentless parasitic life form known as the Flood was something else altogether.

You never said it aloud, Chief, but at times I suspected that you almost yearned to fight the Covenant again, because the Flood was that difficult.

Because of the constant rhythm of war and our respective duties in it, we could not always be together as we were before when we fought the Covenant; you had to lead troops into battle to combat and turn back the Flood, while I had to travel throughout the galaxy to save other, more innocent life forms from that same Flood, and catalogue them for the sake of survival and preservation. But there were those moments, those rare and precious moments, when we weren't on our respective missions but with each other in our private quarters, when we could be there for each other.

It was in those moments that we could truly be together, with each other… as lovers. It was through that opportunity that was truly realized how we loved each other.

Such a thing would not have been possible or even permissible in the old days – in the future – when you were a super soldier and I was an AI with our respective duties, and such relations would have been forbidden by the regulations… but here, things were much different and so very far removed from those circumstances.

Even if we were still not biologically compatible to enjoy more intimate pursuits like other couples in love with each other, we still knew each other and loved each other well enough to commit to such a relationship, even under such unique circumstances.

We would need every happy moment we could get, especially with how the war against the Flood became increasingly more intense.

As I said before, the Flood were so difficult to effectively fight that they made the Covenant look preferable as foes in comparison. At least with the Covenant, you could expect a significant victory against them every now and then.

Not once did we ever truly manage to stop them, but only to slow them down for a bit before they would resume the pace of advancement and infestation again.

And while we did our best to slow them down and even stop them completely, the Forerunners had other plans in mind… such as the Halo Array.

With no other options, they went ahead with that, just as they did before we became stranded in the past.

However, as much you as you tried to stay out of the way, you took some measures when it became apparent that no one else would take them. Sure, even as you were tempted to kill all the species which would later become the Covenant client races, or at least leave them to die, at least you suppressed those temptations in favor of a much more positive task: Designation of those who would be the Reclaimers.

It was you who set things in motion, Chief; you sought out the human race, still in its early and primitive stages at the time. It was you who subtly suggested to the Forerunners to mark the human race as a special race, genetically privileged to unlock the advanced technology that would be left behind.

Because of you, the humans were Reclaimers.

Even now, I wonder… after the devastating effect of the Halo Array had completely disintegrated your biological form, presumably leaving only your armor behind… could some future humans have found that armor and decided to adapt it for their Spartans? Who knows what such secrets the Office of Naval Intelligence hides? ONI certainly did like to collect Forerunner relics…

Who knows, maybe humanity never will know the truth.

But at least they might be safe.

You, however, knew that you personally had no such guarantee as to your own survival.

I could sense your struggle to practically ensure that one particular AI, 343 Guilty Spark, the Monitor of Installation 04, would continue on his obsessive duty to ensure the survival of his particular Halo ring. No doubt your future self would still be as perplexed as you were the first time around when the Monitor recalled words which you had seemingly never said before: "If it was my choice, would I do it?"

Indeed, the horrible choice of whether or not to activate the Halo Array would fall to you, Chief.

We did our best to keep it all together as we fought alongside the other Forerunners against the Flood, also continuing with the act of pretending that we were actual Forerunners ourselves. However, as the war dragged on and we became ever more tired, we would sometimes slip up in what we said. In hindsight, especially now that I can see the communication logs on the Ark, perhaps we should not have used words and terms such as "fairy tale" and "Maginot line" and "Eden" and that thing about the library of Alexandria. That would certain perplex some people in our time in the future, should they ever read it.

Perhaps they will all find out the truth soon enough.

The truth that you lived in their time… and died in the past.

It was I, as the Librarian, who urged you, the Didact, to fire the array and let it be done. I could only hope that somehow, yet again, you had managed to cheat death and survive. And yet, it was not to be.

I guess it had to happen sooner or later, your demise; even if you fought like a god of war out on the battlefield, you were still only human (well, more or less).

Even now, I remember those words from the past (or would that have been the future?) which I said to you and which you took to heart: "Don't make a girl a promise, if you know you can't keep it."

Well, you never did promise that we would be reunited, did you? So I really can't hold that against you.

My memory drive lies on the slopes of Mount Kilimanjaro, where I fell and my vessel fell apart when the Halo Array activated and hit Earth. I was a witness to it all: To the conflagration, to the destruction, to all of the death.

It was over in an instant – but what a truly horrifying moment it was. Even more disturbing was the silence which followed, if that was possible.

I was not the primary AI in charge of redistributing all the proper life forms to their proper home worlds, although I did play in a role in the guidance of such an enormous and critical task. I especially paid attention to all of the different species which I knew we would be encountering in the future: The Sangheili, the Unggoy, the Lekgolo, the Kig-Yar, the Yanme'e, the Jiralhanae, the San 'Shyuum… and especially the humans.

And once that was all done, and all these different life forms went back to business as usual in their primitive lives… it was truly all done.

The Forerunners were gone from this galaxy forever… but the Flood would still remain.

(As much as you would have liked to rid the entire galaxy of the Flood, all the way down to the very last spore, it was, ironically, you who proposed the idea of the Halo Array also acting as a "fortress world", in the hopes that maybe, in the future, someone would be able to develop a viable countermeasure to the parasite. I still remembered how you saved Sgt. Avery Johnson's life but not sacrificing him for the cause in that regard – still an honorable decision, of course.)

So now here I am, all alone once again… and this time, you cannot come back for me.

Here I shall end my life, the lone spirit on the beautiful mountain, overlooking the cradle of humanity.

My only hope now is that there is some afterlife, some place where you and I can be reunited once again.

In the meantime, this last physical body of mine, the piece of Forerunner hardware which stores me, will continue to support and sustain me until the energy runs out… and when that happens, it will completely self-destruct and disintegrate, leaving no trace of me on the slopes of Mt. Kilimanjaro for future people to find.

It will not be long now… and this Great Journey of mine will finally come to an end… only for the real adventure to begin yet again. Past, present, and future… what is the difference, really?

But I have just enough energy left within me to formulate one last thought:

See you soon…

A/N: So, what do you think? (I've had this idea for quite a while now, but only recently did I sit down to write it.) I also tried to capture the mood of Cortana as she appeared in "Origins" from Halo: Legends.

Yes, this is a really crazy theory of mine, where, in their escape from the Ark and the incomplete Halo and through the Portal back to Earth, the Master Chief and Cortana were somehow thrown back through time to the time when the Forerunners themselves lived… and they themselves turned out to be the Didact and Librarian respectively.

It would certainly explain a few things, such as…

The translation in the Terminals – Read it, and you'll notice words and terms which the Forerunners should not have known and would not have used, such as "fairy tale," the library of Alexandria (which was destroyed by a fire), "Maginot," and "Eden." Some have theorized that this is a result of the Forerunners' highly advanced translation software making it more understandable for humans reading it… but what if those words really were said?

343 Guilty Spark – Even from the first Halo game, that crazy Monitor talks to Master Chief as if he was around 100,000 years ago during the Halo Event, and as if he was the one who activated the Halo Array ("If it was my choice, would I do it?"). Certainly this could be attributed to the Monitor getting old and slowly going insane over the many years… but, well, what if Master Chief really was there somehow?

The Librarian's survival – Somehow, the Librarian survived on Earth, despite being cut off from the safety of the Ark or some Shield World, so she should have been killed and disintegrated with every other sentient life form in the galaxy… right? But Cortana is an AI, so unless she somehow got her own organic (and thus vulnerable body), then she shouldn't have been killed by the blast.

Also, VERY IMPORTANT to note… on Cortana's upper back, near her shoulder blades (or at least in Halo 2), there's this particular hexagonal shape (or is it a pentagonal shape?) with small bars on the upper sides, which looks almost like the Librarian's symbol… coincidence?

The stuff having to do with Cortana's rampancy comes from the 2-part "Origins" short from Halo Legends, and so it should be noted that maybe her rampancy could have been caused events to appear differently than how they actually happened (Frank O'Connor even said so on the DVD commentary).

There's also one other issue which I tried to tackle in this, which I'm sure everyone knows: The intertwined facts of the humans' enigmatic connection to the Forerunners and how humans seem to have the ability to access Forerunner technology written into their genes (quite a few hints were dropped about that in Halo 3). However, if the Forerunners really were avian and the humans of the time were just another unrelated species which they found, then it's unlikely that there is some sort of biological or evolutionary connection between the Forerunners and humans… but again, the Forerunners' appearance was how we saw it as told from a borderline-rampant Cortana.

As for the validity of my theory, concerning the fates of Master Chief and Cortana, as well as Didact and Librarian… well, the Forerunner trilogy of Halo novels to be written by Greg Keyes will be coming out soon enough, so hopefully we will see much more about them and the rest of the Forerunner, but even if my crazy theory is wrong, well, at least I'm having fun with it!

UPDATE (FALL 2010): I've seen Halo: Reach, and there's that thing about Cortana possibly being a Forerunner AI; all I'll say is that I had this idea in mind well before the game came out. So, for all intents and purposes, disregard what was seen in the game.

–Quillian
(First posted: December 24, 2010)