Everyone here has some awesome ideas, and setting up this thread to discuss crazy ideas was a great one. Here's a few wild theories that I've cobbled together on my own or from the thoughts of others. If you deserve credit, let me know. Oh, and beware, there's a lot of
SPOILERS FROM HALO 1 AND 2. Just in case everything wasn't spoiled already:
It could have been a Forerunner who fired the Halos, and that same forerunner could be the one who "killed" AdjutantReflex. Through cryogenic sleep or having his brain mapped into a "smart AI" like ours (but with a longer lifespan) he could still be around in our time, on the ark or any installation. Remember that Miranda Keyes removed the index from Delta Halo (Installation 05) right before it fired, so the countdown can be interrupted from the initiating Halo without the need of being physically present on the ark to cancel the firing.
A note on this Forerunner: He/She/It might have murdered their entire race on purpose. They had made plans to survive, but their shelters were empty. They had even contained the flood for future study and specifically to keep it alive - if something that was going to eradicate their entire race could be annihilated, why would they make certain that it would survive until someone else found it? Maybe they weren't expecting the Halos to fire so soon, or fire at all. Perhaps they left them there as a last-case scenario, with prerecorded messages of their defeat (the one who fired the device in the log needs not be the one who left the message in the video) - but what if they were simply betrayed at the moment of victory by one of their own? What if one of their own BECAME the gravemind? We've already seen how one was using Keyes in an irregular fashion. What if that was the beginning of a gravemind? And what if this Forerunner became the gravemind by choice, and retained control?
Another idea: The one who fired the Haloes said:
All I have left is the quiet of space to lull me to sleep. /
No pain. No remorse. Is that normal?
AR asks,
What has he learned in Eon’s slumber?
I doubt it’s mercy or sorrow.
Seems to support the idea that the one who first fired the array is now attacking AR.
The quote "Something that once was malevolent is stirring" could be the Flood (and/or Gravemind) waking up from the Covenant prodding them on other Halos perhaps. We don't know the range on their hive mind capability, but the ones in Halo 1 were awake when we got there, correct? Did the Covenant wake them up right before we arrived, or were they stirring long before? Another possibility is that the appearance/awakening of AR and this malevolent being could be linked to the time travel slipspace disturbance from Melissa in I Love Bees, if that story is allowed to be related. Probably a no on that one, given Bungie's iffy stance on "is it canon or not?"
And correct me if I'm wrong, but it's never stated that the Covenant have only visited the same two Halos as we did, or that they never saw the Flood before. They just couldn't fire the array without a reclaimer (read: human) anyway, and they certainly know their way around the technology. Two possibilties here: Either they can fire the array from the Ark without a Reclaimer, and that's why they want to get to it so desperately, OR the Prophets know that it's a safe haven, and want to secure it for themselves. It's shown that they already understand the Great Journey is going to wipe the galaxy of sentient life, and maybe they don't want to die.
Anyway, AR notes:
An older life is here with us. He is not as helpful as I. His motives are oblique and his alliances opaque.
He plays with time even as he hides in its folds.
He outranks me and anyway, is stronger.
This supports the idea of a Forerunner as the entity that "killed" AR. He outranks him. If this Forerunner became the Gravemind and retained its identity, it could still possibly outrank him. And you don't need to be an AI to delete some code. Even the Flood could interact with technology, and the Gravemind seemed to have the ability to use Delta Halo's teleport system. You don't even need to be present for tat matter, and obviously the Halos can communicate with each other (shown after Delta Halo's firing sequence was aborted and it sent an automated command to all other Halos). Why shouldn't they be in contact with the Ark as well? And why couldn't AR be deleted locally OR remotely? This shadowy figure could be "here with us" figuratively, watching from behind the scenes and interfacing at a distance. Remote desktop, anyone?
Another idea is that N'chala, the tribesman from the comics, was the one who activated the array of Halos. As the flood overtook the Forerunners before they had a chance to get to their shield planet bunkers, a monitor told him to fire the array to fix things.
And unless the monitors share a single intelligence (which doesn't seem likely given Guilty Spark and Penitent Tangent's actions), Guilty Spark WAS present at the time of the original firing, either physically or through a communications link. The question was asked of him, "What should I do? If it was your choice, would you do it?" He responded "yes," as the events of Halo 1 seem to show.
Also, they seem to see all human life (and possibly all non-flood life) in general as a collective. They automatically assume that the reclaimers know how what the Halo is for, and that they remember what the first reclaimer did. This is shown by Guilty Spark when speaking to Chief, and Penitent Tangent when speaking to the Arbiter. That supports the idea that a human fired the array in the first place - unless, of course, Forerunners were seen as reclaimers too. Or possibly, Forerunners were also human, which allows for the first firing to be performed by a Forerunner.
Anyway, I see now that I've gotten carried away with myself and rambled on far too long. Please find the holes in these arguments so that I can edit and delete parts to make it shorter.
EDIT: Several quotes point toward the malevolent force being a machine or AI - possibly the Forerunner turned into an AI construct? Anyway, from AR:
He was always better than I.
More powerful.
More intelligent.
A better machine.
Adjutant Reflex is terminated.
Attempt no further communication.
I am utilizing its matrix.
Everything is within protocol.
The mercy and sorrow quote still leads me to believe there's a non-machine brain hidden behind it all. And it wouldn't be a stretch to call the Gravemind and the flood a "machine." After all, we speak of a "war machine" when we describe an army composed of many people.