In my mind, given that Hephaestus has taken control over some Cauldrons but having failed to control others, due to humans destroying machines essential to ZD would lead to Hephaestus deeming humans a threat to the survival of the Terraforming System, brief connection with the other Subordinate Functions alongside GIAI and the FZ Printing Matrix could have led to to discover NEMESIS or it could independently discover its existence, maybe by using the global distribution of Tallnecks data monitoring tools to detect NEMESIS entering the solar system
That could lead to Heph coming to the conclusion that NEMESIS would ultimately be the bigger threat to Earth and the Terraforming System, as whilst the occasional human would destroy its machines and individuals having a small impact on the overall survival of the Terraforming System, NEMESIS would seek to destroy everything without exception, possibly leading to Heph becoming something of a reluctant antagonistic morally ambiguous ally to Aloy, in that while Heph maybe in the latter part of any fight against NEMESIS it would still seek to remain independent of GIAI,
With the possibility that in the absence of Heph it would lead Aloy, both before and after any hypothetical alliance between Heph and Aloy against NEMESIS, as it was suggested during its escape from FZ, that Heph’s functionality could be replicated in some form, with the possibility that Beta would go through different ZD facilities to find the original code for Heph and create her own version of it, maybe named Vulcan after Hephaestus’s mythology Roman counterpart, maybe even with such missions resulting in sections of Horizon 3 where Beta would be playable in some capacity,
In addition given that according to CYAN, of the some Cauldrons in the global network had not fallen under Hephaestus‘s control due to their cyber defences being so strong that Heph was unable to break through, could mean that there might be some areas of the world that have not yet experienced any significant threat of the Derangement and its machines still functioning as before NEMESIS sent its signal, with the possibility that if NEMESIS was capable of breaking through the unaffected cyber defences of those Cauldrons to produce its own machines, with its capabilities to print new machines being greater than Heph and in a digital battle for control of the world’s Cauldrons, if Aloy could not prevent both AI’s from having control over them, and that an alternative AI had not been created, she might be forced to reluctantly accept allowing Hephaestus having control over the entire network, if only to deny NEMESIS control over them and with Heph being compared to the technology of FZ slightly less powerful and more within the range of most peoples ability to handle, with Heph capacity to create new machines being substantially less than the ability of a printer of FZ and NEMESIS,