Alpha Complex is on Post-Fall EarthFriend 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 Factors were the only other species in the galaxy to survive their SingularitySome 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 ETITheir biochauvinism is attempted memetic warfare to prevent transhumanity from ascending to the ETI's level.
The Pandora Gates are trapsSimilar 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 ETIThey'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.
Watts-MacLeod is a benign mutation of the Exsurgent VirusIn 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.