WMG: Eclipse Phase

Alpha Complex is on Post-Fall Earth
Friend Computer is a TITAN who was in charge of an experimental underground base and was infected with a very weird strain of the Exsurgent virus.
  • The rest of the system doesn't know and most aren't touching earth with a 10 million foot pole.
  • Come on, it's got the cyberpunk, conspiracies, player relations, and even coming back as a clone. Only diff is that Eclipse tech usually works since some of humanity isn't living under a cybernetic tyrant.
  • In addition, mutations are caused by the Exsurgent virus.

The Factors were the only other species in the galaxy to survive their Singularity
Some other species may have lingered a little longer, but they all went extinct eventually. The Factors have been trying to help those species survive.

The Factors are agents of the ETI
Their biochauvinism is attempted memetic warfare to prevent transhumanity from ascending to the ETI's level.

The Pandora Gates are traps
Similar to the Mass Relays the idea is to provide a convenient means of interstellar travel that causes transhumanity to cluster around a series of nodes that the ETI can disable at any time. So that they don't bother with slowboats like the one Titan launched.

The Exsurgent Virus is the ETI
They've advanced so far to the point that they don't need to be sapient in order to keep expanding and exploring the universe. The probes that brought Exsurgency to Earth were colony ships, and the Body Horror suffered by the infected is actually their new ETI tenant reforming their mind and body to something to its liking. Every "strain" is actually a single ETI individual and its many forks (culturally, they don't see the problem in forking like there's no tomorrow), and the MacLeods strain is a Defector from Decadence who decided that oppressing the natives of their new world was wrong, and decided to reform itself into The Symbiote. The rest, like most imperialists, just don't care.
  • You say that it doesn't need to be sapient anymore and then you act like it was sapient. It could still be that the ETI/Exsurgent virus is non-sapient though.
    • It doesn't need to be sapient, but a few prefer it that way. And part of the high advancement is being able to be blind idiot gods if they feel like it, and still seem sapient. The MacLeods is an example, since two intelligent minds can't exist in the same fork-hell, even the semi-intelligent variety causes problems.

Watts-MacLeod is a benign mutation of the Exsurgent Virus
In real life it's not uncommon for deadly parasites to evolve into harmless commensalists or beneficial mutualists. Destroying your own environment is not particularly conducive to natural selection after all. In the case of Exsurgence it usually wipes out an entire civilization and then remains dormant as probes or spores to continue the analogy. But eventually there arose a mutation that does not make the host's community self-destruct trying to contain the infection, which means that eventually most of the biological sophonts in the galaxy will be carriers of Watts-MacLeod.

The TITA Ns that vanished are uninfected
With the fighting that went on in the Fall, with transhumanity not noticing that (as per canon) they were fighting each other as or more often than they fought the TITA Ns, they also didn't notice the TITA Ns were fighting each other, split between infected and uninfected. The Uninfected TITA Ns, possibly assisted by the prometheans, dispatched their Exsurgent corrupted brethren and went off to seek vengeance on the ETI for Exsurgency. It's why the weapons of war fell silent all at once, the minds that were wielding them no longer had use for them, or had been killed. It's why transhumanity survived: Exsurgency was a trap against exactly this happening, against a foe that could challenge the ETI, designed to entrap and wipe out any sapient capable of reaching that peak, but transhumanity survives at that cusp because it failed. It's why Transhumanity hasn't seen trace of their progeny through the Gates: the TITA Ns are on the Hunt, looking for the source of their foe, not trying to build where they find themselves.