Sid Meier's Alpha Centauri/WMG

Aki Luttinen had parental issues

 * She has a name that would be perfect for a Finnish...boy. Her father wanted a son instead of a daughter and therefore named her that way. Being The Unfavourite resulted in her dismissing all emotions as fickle and unreasonable. The algorithm incident was a deliberate attempt to free herself from those flaws of humanity.

Morgan Industries is quickly defeated as an independent faction, keeps going regardless

 * Morgan's pacifist and has natural penalties to Police and Support, so he probably doesn't last long. Perhaps he's conquered but acquitted of any potential war crimes and allowed to lead his company. Alternatively he may voluntarily submit to Lal or Provost, becoming a quasi-client state.
 * Or the government and business are separate entities, so when he steps down as leader of the Morganites, he just runs his megacorp.

The UN is aware that Morgan is planning to sneak on board the Unity

 * Just like some of the characters pointed out in one of the prequel novels, sneaking on board the Unity is not an easy task. You will need to have your own pod for the 40 year cold sleeps as well as an individual power supply. Although Morgan's company was been contracted to build part of the ship, it is unlikely that not a single UN official noticed that he added in the extra parts for himself. The UN is likely to be either powerless to stop him due to how critical he was to the operation, or simply decided to not do anything about it.
 * Given who he was, he might have smeared hands of anyone from the Secretary General to the lowliest floor sweeper until he made it work.

The canonical storyline is: Deirdre is the protagonist and completes the Ascent to Transcendance
Outside-of-game media aside, the interludes are clearly conversations with planet. Much of the game makes no sense if, for example, you play Miriam and have your protege meld with a mindworm boil. In addition, Miriam ; Zakharov ; and Santiago. Less ominously, Yang and Morgan stop contributing to quotes after tech level 10 or so, having little to nothing to say about some rather momentous events. Plus, if you look at them all, an environmentalist and humanitarian who occasionally crosses the line into ecoterrorism is at least a few steps ahead of a Mad Scientist, Corrupt Corporate Executive, Knight Templar, Evil Overlord, and Colonel Kilgore. There is, of course, Lal, but some of the technology that makes the Ascent possible clearly offends his sensibilities due to its potential for abuse.
 * Made even more obvious since Deidre provides the quotations for the Ascent to Transcendence and Transcendent Thought projects.
 * Morgan stops contributing to quotes after tech level 10, but Morgan Industries keeps being quoted, implying that Morgan either retreated from the public or was ousted by T.M. Morgan-Reilly.
 * My guess: Dierdre and Lal are Pact Sister and Brother, with Lal distinctly the junior partner, maintaining an uneasy peace with the Morganites. Morgan himself is retired, giving the responsibilities of management to his son or nephew (T.M. Morgan-Reilly). The University probably still exists, but Zakharov's post-Lab Three campaign against the mindworms earned him a Gaian-Peacekeeping "police action," with one of his underlings (Petrov, perhaps) being installed as the new Provost. Yang and Miriam are probably seriously weakened, and it would be highly realistic for them to be hated enough by the Gaians, Peacekeepers, Morganites, and University for them to be the pariah states of this world--and come to think of it, let's just compare the Hive to North Korea and the Believers to Iran. In the end, Dierdre Ascends, with Lal joining in (per the Pact), and Morgan goes back to recolonize Earth.
 * Equally possible is that Zakharov's  was just a Heroic BSOD and he got better. As he's the one who describes the events leading up to the transcendence and is the best candidate to figure out how to break the ongoing cycle, he has to have been around and instrumental to the process up until at least that point. Perhaps a tri-lateral pact between Dierdre, who was the one in tune with Planet, Lal, who had the military firepower to support the alliance without Santiago's extremism, and Zakharov, who had the scientific knowledge and logical outlook to figure the whole transcendence thing out?
 * Considering that the game allows trilateral cooperative victory and survival of surrendered factions, it is safe to assume that Lady D, Zack and Lal are the three deities of Chiron, while the others are either destroyed  or have surrendered to the pact.
 * Concerning Zak, since he aims for research, he will usually pick Knowledge and Cybernetics as a Social Model. Guess what other benefits Cybernetics has. +2 Planet (which also allows you to catch the worms, he condemned so much after the Lab Three incident). Which probably enabled him also to speak with Planet. After constructing "Voice of Planet", he is quoted from his work, which is aptly named "Planet Speaks", which is also the only quote, this work provides. Given that Cybernetics is a late-game social model, it makes sence.

Most of the crew members on the Unity are either Templars or Assassin.

 * The decades of war and unrest during Earth's final days most likely resulted in all the Pieces of Eden being either destroyed or lost. Also, it became clear that civilization on Earth is come to an end. Thought the centuries, both groups have already infiltrated most of the world's influential organizations such as the UN. Therefore all they needed to do was to preserve the best and the brightest of their members so they can continue the fight somewhere else. This was the start of the Unity Project. Ones they get to Planet, the Templars discovered how the fungus network functions and the possibility of what they wanted all along by means of the Ascent to Transcendence. The Assassins, on the other hand, will do everything in their power to stop them.
 * This makes Deirdre, Yang, Zakharov, Aki Zeta-5, and (possibly) Cha Dawn Templars. And Morgan, Santiago, Miriam, and Domai to be Assassins. Everyone else are just normal people that got caught in between.
 * What about the Manifold Usurpers and the Manifold Caretakers? Or are they above the whole thing since they're aliens?
 * Either that, or they were The Ones Who Came Before who created the Pieces of Eden and created humanity in the first place.
 * Alternatively, everyone is a Templar that left after a Piece of Eden malfunctioned.
 * I disagree on who is a Templar and who is an Assassin. The Templars would be associated with Earth-based power structures, whereas Assassins would doubtless be opposed to those old power structures. Thus, the Templars are likely Yang, Morgan, Lal, and Miriam. Assassins would be Deidre, Santiago, Roze, and likely Svensgaard. Zakharov, Domai, and Aki Zeta-5 could be in either camp.
 * Zakharov will likely be siding with the Assassins the same reason that Piri Reis did, since they offer more academic and intellectual freedom to its members compared to the Templars.

The Unity project is part of the Vault Experiment.

 * The Unity project and the Vaults both have the same goal, to preserve humanity after the end of the world as we know it. However, the vaults are actually secret government social experiments to test and study how people react under different unexpected situations. In Fallout 1 we learn that one of the vaults, Vault 15, was full of people that have radically diverse ideologies. Sounds familiar?
 * This could work if the Vaults weren't designed for the purpose of figuring out who would be the best for space travel. I propose that Vault-Tec and the Enclave were planning to replicate the United Nation's expedition to Alpha Centuari by way of vaults.
 * Actually, the Human Hive are a lot like this. Social experiments, underground communes; it all fits.
 * (The OP) Perhaps the Unity project was launched by the UN shortly before it was dissolved. The Enclave was inspired by the Unity project to launch their own space colony program. But seeing as how things went wrong with the Unity, they create the vault project.
 * Well, they wouldn't know that something went wrong with the Unity since the Unity cut off all contact with Earth.
 * The Enclave being who they are, can easily infiltrate the UN Alpha Centauri Mission Comity and sabotage the commutation between the Unity and the rest of Earth when keep monitoring the Unity.
 * This actually makes a shocking ammount of sense given evidence that none of the factions have that much American influence, and its implied when you build an information controlling secret project that the US descended into some kind of dictatorship which fell into anarchy (very similar to Fallout where the same thing happened) its possible that the US government (controlled by the government) abstained from taking part in the Unity project since they wouldnt be the ones to lead the project and also because of the massive chinese involvement in the project.

Whoever provides the quote for a technology/Secret Project/base was to first to build that.

 * Yes, this means Lal built the Mind-Machine Interface.
 * It doesn't make him a hypocrite. Just because the Peacekeepers developed it first doesn't mean they applied it in such a fashion. Hell, he himself had such an interface put in at one point if I remember the quotes.
 * That wouldn't make any sense, since he is quoted from his "Report of Human Rights", where he heavily critizise it.

Miriam believes herself to be Christ reincarnated.

 * In every Believers quote, she only ever refers to the Lord or God, but never seems to mention Jesus Christ. That and her general behaivour seems to suggest that she believes she is the Messiah.
 * Alternatively she's just Jewish.
 * Unlikely, since her profile on the official website shows that she is an Evangelical Christian. A lot of her bases also have names that refer to stories in the New Testament such as He Walked on Water, Loaves and Fishes, Water to Wine, The Rapture, etc.
 * Partly confirmed! Not much as Christ himself, but some kind of prophet. PSI-Gate quotes her from her work "The Last Testament". Either a theological work or an addition to the bible.

Chiron/Planet doesn't actually exist, and the whole story is a collective Dying Dream of the Unity crew in deep freeze.
Captain Garland was awakened by the ship to discover that the Unity was running out of power and had no chance of reaching an habitable planet before the deaths of everyone on the ship. He decided to let the crew die with some sense of accomplishment, creating a simulated reality for everyone on the ship. He opts not to enter, instead choosing to "die" at the begining of the simulation to set off the crew's split. This ensures that everyone gets to join the faction they would most like to live within. The alien factions are just programs to make things more interesting. Garland commits suicide in reality, and 500 years of drifting through space later, the Unity's fusion drive finally gives out.

The Unity project is related to the Golgafrincham B ark
Each faction leader represents what was causing the disastrous events on Earth: multinationals only interested in the bottom line (Morgan), religious, environmental and scientific fanaticism (Miriam, Diedre, and Zakaharov, respectively), totalitarian regimes (Yang), well-meaning but ultimately ineffective bureaucracies like the U.N. (Lal), and the military-industrial complex (Santiago). They were placed on the Unity with deliberately faulty communications equipment, so it seems like there are no further transmissions from Earth.

Zakharov is a reverse Mad Scientist
He is to Boring but Practical what other mad scientists are to Awesome but Impractical, all while retaining the same brilliance and the same sense of ethics.