How exactly would HEPHAESTUS be handled in the third game
So HEPHAESTUS has been supercharged thanks to its encounter with zenith tech and most likely is aware of NEMESIS since it was injected into zenith systems at the end of HFW.
HEPHAESTUS' primary goal has always been to protect the terraforming system no matter the cost (minus its independence) but we can assume that if the reason was great enough, it would be willing to work with GAIA as a bare minimum.
Now i'm thinking of 3 potential possibilities that might happen in the third game.
HEPHAESTUS debates with itself over whether or not to join GAIA is an option since NEMESIS poses a substantial threat, even greater than humans, to its system and sacrifices its independence to save it.
HEPHAESTUS gets captured by NEMESIS due to being part zenith tech now and therefore traceable and subjected to the same or worse treatment that it gave to CYAN and in a desperate last attempt, sends a message across the cauldron network which is picked up by GAIA who then informs Aloy and she along with a few others goes to save it. HEPHAESTUS is then integrated into GAIA to forget what it went through (i'm guessing Heph is easier to control then reawakening the faro plague and fixing multiple Horus' when they can be easily destroyed when in a dormant state. They may also be used since Walter said that was an option when facing it)
A replacement for Heph is made and the original one is left to be controlled by NEMESIS and destroyed when it's defeated which once again allows GAIA control of the system completely.
I'm just guessing and may be completely wrong but given the fact that Heph is supercharged (maybe, don't know if it's confirmed) and working on a defence against the Omega clearance and the time it will be given to evolve since there will probs be a substantial time gap from the second and third game makes me believe that Aloy capturing will be next to impossible even with 4 of the worlds smartest people working on it.