Oh Miriam's God.
I've just come to the absolutely and utterly most horrific conclusion about Alpha Centauri's race to transcendence plot.
In canon, judging from the various quotes and cutscenes, an official rough timeline of what happens after the landing can be understood.
Chairman Sheng-Ji Yang builds his underground bases. Zhakarov hurriedly starts his research, and successfully ushers in a burst of discovered knowledge. Miriam and her believers colonize the land quickly, spreading religious mysticism. Morgan quickly sets about exploiting planet with the resources ultimately ending in his pocket, creating better and better systems to exploit. Santiago begins expanding and establishing her training doctrines. Deidre studies and observes planet.
A whole lot happens in between for every faction, but in the grand scheme of things much later after planetfall Morgan destroys Provin Lal and the Peacekeepers while Santiago's making great military discoveries like the mastery of ocean/air travel and the command nexus, and Morgan makes economical discoveries. Someone takes out Morgan [could be anyone, as Morgan fought for and against whoever profited him the most], probably Sheng-Ji Yang, Deidre or Miriam - all three have the means to do so, and if you consider the Data Angels to have never split off, then there was a small group of hackers who could have very well destroyed Morgan industries from within as well by crashing the economic system on which Morgan's networks relied on [especially when you consider that after the Network backbone - we do not hear from Morgan again, suggesting that placing his business on the reliance of the Network contributed to his destruction]. Zhakarov meanwhile continues research and begins technologically advancing far beyond all other factions at this point, [re]discovering space travel, matter transportation and advanced theories made into scientific fact.
That leaves Planet with the Spartans under Santiago, the Believers under Miriam, the Gaians under Deidre, the Hive under Sheng-Ji Yang and the University under Zhakarov.
Yang is probably taken down by the free drones if they too never split off, or perhaps by mind worms. Having turned himself into a brain in a jar, he can do little to stop his ideological system dissolving from internal and external factors.
The Believers and the University begin conflict as the University's technological advances start to take on more menacing shape, like the self-aware replicating nanites, the Believers being led by Miriam strong in their convictions that Zhakarov will destroy the human species meddling with power he is not ready for.
At this time also, Santiago is having trouble with the mind worms. She develops wards to fight off the ever increasing boils and their ability to incapacitate troops with terror - she is the one to employ the neural amplifier.
At some point Sister Miriam Godwinson gains access to space travel [the tech having been stolen from the University no doubt] and the University and the Believers fight on Nessus, Chiron and at the transporters in space, the airs and oceans of Planet, and on the ground technologically advanced University soldiers uplinked to the MMI fight off against fanatic legions of Believers.
Santiago employs more and more high-tech weapons to fight. The Spartans get more and more desperate, employing nanites and armies of clones to combat an unrevealed threat. Spartan cities are shown as destroyed.
The Spartans disappear.
Soon after this it appears that the Believers lost their war against the University and all who dissented were killed. Technology won in the end, and the self-aware colony destroyed the last remnants of Miriam's faction.
Prokor Zhakharov with his vast technological superiority sees the imminent threat of Planet's awakening and successfully manages to avert humanity's extinction with the Voice of Planet discovery.
We no longer hear of him again.
This leaves one last faction left - the Gaians. Lady Deidre Skye narrates transcendence.
Lady Deidre Skye claims she is the one for peace. At first glance, it appear so.
She lives in harmony with planet and keeps her people safe alongside boils of mind worms and locusts, as all frolick naked in the forest's commons.
One of her quotes is about her parking a grav tank next to a bunker to observe the damage from something. Something which caused destruction which "took weeks to assess... There were few signs of human life. Lady Deidre Skye, our secret war." On her work with perimeter defences, she had extensive knowledge of the capabilities of the mind worm and knew what defences they could overcome. She had tested them before.
This isn't even a huge leap from assumptions. There are a few factions where it could be disputed whether or not Deidre had a role in their destruction, but look at the way she phrases things.
"There were few signs of human life." There are talks of bunkers, wrecked buildings and even the electronics broken up. This could have been the destruction of Morgan industries or the Hive, or perhaps a Spartan city. Judging by the description of cannon ports, data cores and shields it was likely a hive city - at the proverbial hands of an alien attack. Mind worms.
Deidre would have reason to invest in the downfall of Sheng-Ji Yang and Morgan, as both enjoyed industry at the expense of planet.
Once both are out of the way, she begins consolidating her power. Sheng-Ji Yang was the only faction who boasted anti-psionic capabilities, and his entire ideology was about controlling the mind - rendering the forces of planet ineffective and impotent.
The Spartans, while not boasting these anti-psionic capabilities did know how to fight - and they used their technology to adapt to fight Planet. This would make the Spartans the only faction at that time to be researching in how to nullify Mind worms.
The evidence that we have for the Spartans having been destroyed by the Gaians, is in that the secret project "The Dream Twister" has an unfortunate person subjected to their worst nightmares, and at the end has the same twisted animation as the mind worm boil's attack in game. It fits the description of a mind worm boil too;
"Richard Baxton piloted his Recon Rover into a fungal vortex and held off four waves of mind worms, saving an entire colony. We immediately purchased his identity manifests and repackaged him into the Recon Rover Rick character with a multi-tiered media campaign: televids, touchbooks, holos, psi-tours-- the works. People need heroes. They don't need to know how he died clawing his eyes out, screaming for mercy."
While under the control of Empaths, mind worms can be targeted at soldiers only - keeping most civilians alive. Yet civilians are always ultimately lost when a city is taken over, and in the worst way imaginable when at the mercy of mind worms.
Where it goes full cruelty is when you consider the fact that there were no civilians in the Spartan's society. Even the children were soldiers, hence why "there were few signs of human life."
We don't even know the full extent of destruction Deidre caused.
It gets worse.
They are only able to discriminate between soldier and civilian under the control of a human Empath.
It is highly likely that Deidre was raising demon-sized boils of Mind worms and setting them free near whatever faction posed the immediate threat to her. And by doing so she was also subjecting every single human life - civilians included to mass genocide with the worst possible death imaginable, as the mind worms would literally project the worse possible death imaginable into their victim's mind as they burrowed into their brain. The last transmission from Assassin's redoubt, the Spartan capital went as so:
"Mary had a little lamb, little lamb, little lamb.
Mary had a little lamb,
Whose fleece was white as snow."
They fought to the last and all went insane, or worse. Mind worms breed by implanting their eggs within the brains of their hosts. To breed more mind worms, Deidre needed more hosts.
In doing so she always maintained her "pacifist" stance to every other faction - by only ever directing mind worms and setting them free, it would give the illusion of wild attacks as no empaths could be spotted. This would also mean the mind worms killed everyone they overwhelmed.
When Zhakarov discovers the voice of reason, normally he would be able to research much faster than the Gaians. But either Deidre sent the mind worms directly or else released them near his cities, either way she would have been able to research freely whilst Zhakarov diverted his resources to fighting Planet's native life forms and researching to transcend. Whether the University survived or not is quite irrelevant at this point, as Deidre assumes dominant immortal mind with planet and all who are subsumed by the consciousness are beneath her.
Even Sheng-Ji Yang gave human life worth in that it was capable of giving meaning and attaining skills to creating a communal good. Deidre's background quietly mentions that also as a result of her abandonment by her various parents and adopted families/schools, she became introverted and detached from normal social relationships. I don't think that was the extent of her mental seclusion.
I'd go so far as to say she became detached from the human condition altogether.
This is all the true meaning of her secret war.