Civil War Makes Odd Bedfellows
I think it possible that, assuming such an alliance will exist at all in Halo 3, it may only be evident during a portion of it.
From the closing sequences of Halo 2, it seems that there is still some fighting going on at Earth; meaning that some of the fifteen ships that Regret brought with him remained there while he fled to Delta Halo.
Truth is now arriving aboard the Forerunner ship. His ship may or may not still have Elites and Brutes aboard, fighting amongst themselves. In either case, the Master Chief is not actually aware of the potential for this alliance. During the only contact he had with the Arbiter, the Arbiter did not seem willing to admit that Halo was a weapon. While he is aware of the fighting between the Covenant because he observed it during High Charity and Cortana informed him of fighting amongst the Covenant Fleet, this by itself does not necessarily mean that hostilities against humans would lessen.
Likewise, any Elites on board the Covenant ships at Earth may not be aware of the infighting. So it is possible that, early in Halo 3, playing as the Chief, that the primary enemies will still be the usual mix of units, regardless of the civil strife among the Covenant as a whole.
The small force that Regret brought with him was insufficient to subdue the Earth because he was not expecting to find humanity there. As it was, he was lucky to be able to find what he needed and get to Delta Halo, assuming that he obtained the location of Delta Halo from some artifact or information on Earth. It is difficult to imagine why he would go to Earth first and then to Delta Halo if he already knew where it was. Additionally, Truth and Mercy only show the Delta Halo to the Arbiter after Regret has left Earth-- further circumstantial evidence that they were not aware of its location until then.
That force, if it still exists, must be hard put to resist all of the human defenses at Earth. Even were it to be reinforced by the Covenant fleet from High Charity, that fleet itself is in a state of conflict and disarray, so assuming that the struggle is roughly equal on both sides, at most Truth could hope to get support from half of it. If half the fleet left High Charity to assist Truth, it seems likely the rest would follow them there to continue the fight; especially as it seems the fight is mostly motivated by a perception that the Brutes have usurped the Elites' place in the Covenant and thus perhaps jeopardized the latter's chance for a place in the Great Journey.
So this would mean a stalemate, with the addition of Truth's ship plus 15 cruisers to the Brute's side, and all of humanity on the other. It may be that this is the scenario Bungie is trying to create-- a situation in which it is reasonable that the Covenant can be successfully resisted in a space battle. Up until now, the only situations in which humanity was able to achieve such a victory was with overwhelming force or trickery (such as the Keyes Loop).
So, is there going to be a Human-Elite alliance?
I think if there is, it will be quite limited. Bungie showed in Halo 2 that they were willing to make cosmetic alterations to existing units in order to make battles between like units possible when they created the "Heretic" outfits for Elites and Grunts used in Halo 2.
I think it likely that there may be situations in Halo 3 where the Chief and/or the Arbiter fights with the support of both human and Covenant elements against other Covenant units and/or possibly Flood. But I do not think it will be a monolithic conflic where all Elites are on the side of the humans. They all might be willing to rebel against the Brutes because of the betrayal of the Elites on the council, but it seems a stretch to me to think that all the Elites will ally with the humans because of this.
The most likely scenario for that happening involves the Elites being rallied to the cause of the humans, either by the Arbiter, or Half-Jaw-- most likely by the efforts of both combined. Yet when Halo 2 ends, Half-Jaw has taken his cruiser back into the space battle around High Charity to fight against the Brutes, and the Arbiter is stranded in Halo's control room, seemingly without transportation. Keyes and Johnson are with him, so it seems that at least the seed of an Elite-Human alliance is in that room with them.
However, it seems that at least for the moment they may be stranded without transportation. The condition of In Amber Clad is not known, but at any rate, it's crashed on High Charity, which is infested with Flood; so that is probably unvailable to them. If they do decide to use the IAC to escape, look forward to an early Maw-like level where you have to clear the Flood out.
Truth is at the Earth with the Chief, but as far as we know, only Keyes, Johnson, the Arbiter and 343 Guilty Spark are aware of the fact that the system of Halo rings is now in standby mode and can be activated from the Ark; so unless they can communicate this to Earth the necessary sense of dramatic urgency might be missing. The Chief doesn't even know this, and although we might hazard a guess that Cortana becomes aware of it, it hadn't happened yet when the Chief stowed aboard Truth's ship, so she can't have told him.
It is a widespread assumption that the Ark is located on or near Earth. Regardless of where it is, it isn't at Delta Halo. So if our three heroes of Delta Halo are keen to stop the installations from being fired, they have to find transportation to go to the Ark. If that means to Earth, then so much the better for those characters to continue interacting with the Chief-- either directly or indirectly. If those characters aren't involved in that effort, then it's likely they'll be involved along some other story axis-- perhaps the Covenant civil war exclusively.
Then there's the question of Cortana. The Chief says he'll try to come back and get her, but if the Arbiter, Keyes and Johnson are leaving the Delta Halo's system it makes more sense for them to fetch her, assuming that's possible. But while she's aware of their positions and movements because of their neural implants, it doesn't seem as if she can communicate with them through those. So Johnson and Keyes seem unaware of Cortana's present whereabouts or situation, and are likely also not aware of the Chief's unscheduled return to Earth.
Besides, with High Charity apparently under the control of Gravemind and teeming with Flood-- not to mention whatever remnants of the Covenant presence from both factions still surviving that haven't yet succumbed-- a rescue operation to retrieve Cortana might not be possible. Or perhaps that will be the Arbiter's first mission. Hope you liked the level "High Charity" because Halo 3 might very well open with a repeat of that. Given the backlash against Halo 2's early departure from Earth, if the entirety of Halo 3 does not take place there, one can bet that Bungie won't front load all the Earth-based levels early in the game the way they did with Halo 2.
Too Shocked For Words... Almost
You can't imagine how exciting this is! To have a record of all of our lost time! Human history, is it? Fascinating.
Along with Guilty Spark's constant referral to the Master Chief as "reclaimer", this line about "human history" is one of the most-oft cited evidence for the theory that Humans are Forerunners. I've always felt the alternative explanation is much better: that the "lost time" is the time since the last detonation of the Halo system. Given that this detonation should have destroyed all sentient life in the galaxy, any civilization that arose in the meantime would have a history that covered exactly that period, the period since Guilty Spark and the other monitors would have had no contact with their creators, the Forerunners. So the monitors "lost time" matches up quite nicely with the history of human civilization, even if there is no other more explicit connection between the two at all.
Less attention is usually paid to something I think is far more salient, which is Guilty Spark's bemoaning the Chief's willingness to destroy the historical record, and presumably Cortana, along with the ship.
What the line does, though, is forge a possible connection between Halo and some of its early source material. In this case, I don't mean Larry Niven's Ringworld, but rather the Culture stories of Ian M. Banks, among them Consider Phlebas, part of which takes place on an Orbital that resembles Halo far more than Niven's titular structure, and focuses in part on a conflict between the culture and a species of physically imposing, near-immortal religious zealot warriors called the Idirans. Despite not being exactly humanoid in shape as Elites are, there are a lot of similarities between Idirans and Elites.
One of the defining differences between the Idirans and the Culture is their attitudes towards artificial intelligences. The Culture are nominally ruled by their AI constructs, as a nomadic civilization that lives on countless orbitals and ships, each of which is run by a Mind or group of Minds that are exceedingly advanced artificial intelligences. This is something of an offense to the Idirans, who believe they have a manifest destiny given to them by their beliefs; a belief in which sentient artificial intelligences have no place in the universe, let alone the exalted place the Culture put them in.
That Guilty Spark should accord so much important to the PoA's computer records has always seemed strange. Certainly, the PoA's systems themselves would not seem at all impressive to the Monitor, and thus from his perspective having multiple copies of such records should not seem at all strange. Certainly there is nothing to suggest that the PoA's computer files would be at all unusual, so we can easily imagine that any other UNSC ship would have at least as much historical information.
Indeed, given the PoA's special mission, which was originally to be involved in a mission to hijack a Covenant ship en route to the Covenant homeworld and thus kidnap a Prophet to ransom him back to the Covenant in return for a parlay, one might assume the PoA would have less information about humanity and Earth on board, for fear that such information would fall into Covenant hands if the mission failed. Certainly this is foremost on Captain Keyes' mind at the start of the game, as the information about Earth possessed by Cortana must be removed from danger of capture by the Covenant.
These two points I've always found to be in direct opposition to one another, and form one of the worst plot holes in the Halo series. As a counterintelligence AI, it is Cortana's job to break into enemy systems to gain information from them and give the Master Chief an advantage in combat by manipulating those systems.
She does this throughout the course of the game, accessing both Forerunner and Covenant systems.
However, if Cortana herself is in possession of such sensitive information about Earth's location and defenses that she cannot be allowed to fall into enemy hands, how can such information possibly be risked so much as to deliberately place her within the enemy's own systems?
Bungie attempts to cut us off at the pass with this objection, putting our words right into the mouth of 343 Guilty Spark:
Ridiculous! That you would imbue a warship's AI with such a wealth of knowledge! Weren't you worried it might be captured? Or destroyed?
We probably should be. Especially if that AI's job brings her into direct contact with alien systems, thereby increasing the risk of that information being captured. That the Monitor is worried about it being destroyed is curious. One wonders if the Forerunners were really an intergalactic RIAA, willing to prosecute even those making backups of their own data. Why the Monitor assumes that any data Cortana has access to isn't backed up somewhere else is curious.
With regards to risk of Cortana's data being intercepted, some of these questions are addressed more in Eric Nylund's First Strike, as we see more of Cortana doing her job, part of which consists of making copies of herself, and these copies can contain less of her own personality and memories than the original does. In this way, one might imagine that the Cortana we interact with through those foreign systems is not the "complete" Cortana.
But if not, where is she? In the first level, Cortana is physically removed from the PoA's systems and inserted into the Master Chief's suit. We're led to believe that this is a real, physical move that constitutes the entirety of Cortana's functions, memories and personality, including the sensitive information that Keyes was so eager to get off the ship in order to comply with the Cole Protocol. This same physical process is repeated when the Chief brings Cortana to the Control Room and inserts her into the panel there. From then on until we return at the start of Two Betrayals, there is seemingly no residue of Cortana in the Chief's suit. She doesn't speak to you at all through the next two levels; that role falls to 343 Guilty Spark, starting from the end of his namesake level and throughout The Library.
The narrative duties are carried in 343 Guilty Spark by the recording played by dropship victor 933's pilot, and the mid-level cutscene where we see the gruesome fate of Private Jenkins, who always goes for the needler. The absence of Cortana's constant running commentary, along with the level's sinister soundtrack, is one of the things that makes that level so memorable.
So we presume that the entirety of Cortana, as rescued from the Autumn, is now in Halo's Core. Whether that's safe or not, we still don't know. That Cortana is able to use that position to get the drop on 343 Guilty Spark is still a bit surprising, as he is not only a construct himself, but also, presumably, of superior Forerunner design.
Throughout Truth and Reconciliation, Cortana did interact with Covenant systems, but apparently remotely from the Chief's suit, as we still hear her dialogue throughout. This is in marked contrast to what happens during Gravemind and High Charity. At the beginning of Gravemind, we repeat the gesture of removing Cortana from the suit and inserting her into the Covenant system; again, presumably, whole. From then on she only speaks when present in holographic form, and mentions a force "fighting back" in the Covenant systems. When you attempt to take Cortana back she refuses, saying she has to remain so as not to risk a "remote detonation" of the IAC's engines, her contingency plan for stopping the Flood from escaping from Delta Halo and for stopping the activation of the installation if Tartarus should succeed in his mission.
Why the connection from High Charity to In Amber Clad is any more "remote" than the connection from the Chief's suit to the ship is puzzling. While some have perhaps rightfully pointed out that being in the Covenant system might afford her abilities and opportunities denied her within the contstraints of the suit, one also assumes that there is more risk, particularly from the force "fighting back". This excuse doesn't really hold up. It's obvious that at this point, Bungie wants the dramatic effect of separation between the Chief and Cortana, just as they did for the 343 Guilty Spark and Library levels in Halo 1. This separation may be of continuing importance for the story, as Cortana remains on High Charity with Gravemind and does not, apparently, detonate the engines, despite the apparent risk of Flood escaping the ring.
Next Time: Feed me, Seymour...