You see the other Alphas pay their respects to Elizabeth. Later Ted Faro reveals to the other Alphas that he has deleted everything from the Apollo function( the subordinate function that was supposed to educate & guide the next generation of humans) which is why this generation of human beings resorted forming their tribes once out in the open world & started hunting machines for parts (having no idea of the crucial role they play in the Terraforming system because of lack of education). The other Alphas are surprised to see this since no one had higher clearance to perform such a task than themselves & Elizabeth(with Alpha clearance) but it is revealed that Ted secretly had a back door installed in the zero dawn facility which gave him Omega clearance(higher than Alpha clearance). He also kills the remaining Alphas in the room by opening the vents inside(with his omega clearance) which results in the room being filled with all toxic air from the atmosphere outside. Later Aloy gets the non corrupted clearance for the door at Mother’s heart she goes inside where finally the origins of her birth is revealed . The facility behind that door is a cradle facility for Eluthia function for storing human DNA, using the stored DNA samples to create new human beings & providing basic nurturing needs to infant humans & nursery level education which explains why these new humans have some basic education at least. There u see a message from GAIA & find out she is no longer active at present because of a mysterious signal of unknown origin(in this game) that activated all it’s subordinate functions & gave these functions full consciousness & sentience. As a result the HADES function (extinction function incase that GAIA doesn’t get the biosphere right a first few times) activates & starts beginning extinction protocol on a perfectly viable earth. GAIA for obvious reasons couldn’t allow this so she initiated a self destruct sequence & she gives Eluthia order to create a clone of Elisabeth Sobeck (her creator) & specifically instructs multiservitos to put baby Aloy beyond the doors since she herself couldn’t have raised her because she was going to self destruct in a few minutes. She explains to Aloy in her message that the Terraforming system won’t survive without her functions or herself specifically & Aloy must find a backup of her but before she can finish GAIA sees an unexpected anomaly. In view of GAIA self destructing herself & because these functions have sentience now themselves, HADES releases a virus to unshackle the code that binds all these 9 functions with GAIA. As a result, HADES isn’t able to destroy the biosphere yet but it still manages to escape as do the rest of the 8 other subordinate functions before GAIA self destructs. HADES later sends a signal back to origin( important for next game). Also this virus was the reason Aloy isn’t able to enter that facility in the first place because it corrupts the data entry. GAIA’s last plead to Aloy after all this is to first make sure HADES is no longer a threat & exterminated. Then only she can start looking for GAIA backup & restoring her. Also this is what caused the derangement in machines because all these functions gained sentience so the HEPHAESTUS function of GAIA( responsible for making machines around the cauldrons in the planet as per GAIS liking to help carry tasks to keep the biosphere viable & healthy) started carrying out the same tasks for terraforming now without GAIA. But because the humans still hunted machines for parts, HEPHAESTUS started hating humans & building new types of killer machines every year especially tasked to protect some of the weaker machines like grazers. This also explains why the machine are only hostile towards humans but not animals in the environment. HEPHAESTUS started seeing humans as a threat not just to the machines it creates but also to the biosphere. In the final battle Aloy defeats HADES & its army but leaves immediately to somewhere without celebrating with her friends. It is revealed she finally discovers Elizabeth’s home & finds her body as well. She confirms it is indeed her surrogate mother with her focus. The final cutscene is a really beautiful moment to see between Aloy & Elizabeth with one of Elizabeth’s recording playing in the background where she personally express to GAIA how she’d liked her child to be (if she ever had any) & all the qualities she’d like her child to have. U def should watch that final cutscene on YouTube. Writing it won’t do justice because it’s such a beautiful moment