Horizon Zero Dawn Explained: What Does The Ending Really Mean?
8. GAIA Vs. HADES (The 1000 Year Gap)
Following the creation of Project Zero Dawn, the separation of Operation: Enduring Victory on the surface and the surrendering/volunteering/death of those knowing what had to be done, Sobeck and her team designed the APOLLO A.I. programs (in charge of knowledge, language, human cloning, cryo-preserved seedlings etc.) to spring into life in the future, yet they would forever be governed by GAIA - the 'mother A.I.' that would determine how to repopulate Earth piece by piece.
This was contrasted by HADES, a destructive program that could act as a 'failsafe'; a 'reset button' with its own protocols that would activate if and when GAIA got something wrong in this synthetic evolutionary process.
It was determined that GAIA would attempt to repopulate the Earth multiple times, not getting everything right first time round (evolution is a complex thing, after all), so whenever any aberration would occur, HADES would 'wipe the slate clean' by destroying all organic life, so GAIA can learn from her mistakes and try again.
When all organic life is no more, GAIA repopulates. If she gets something, anything wrong, HADES triggers the apocalypse. Rinse repeat until harmony.
This cycle continues over and over for around 1000 years, until the creatures we see in Horizon are the most 'perfect' produced so far.
Speaking of which...