Ending E and how this games ties into automata ?

[Cyber Von Cyberus]

So I've finally gotten to ending E (having a completely new story and playing as Kainé was very refreshing after having to slog through the same main quest multiple times) and I wondered a few things;

1- Was the Machine Network hiding inside of the tree or is it a different entity ? The way the administrator described the Kainé clones was very much like the cores of the Machines and the memory cube was exactly the same thing as YorHa's and the Machines' minds, as if they used the same OS.

2- What happened to the Replicants before Automata ? As far as I understand, the Replicants are biological beings unlike the Androids in Automata, did they get wiped out during the Alien invasion, or did they simply die out due to the Gestalt Project completely failing and everyone dying from the Black Scawl and Shades going mad ?

3- Was there a significant Android population already existing during the events of Replicant ? Devola and Popola's backstory in Automata implies that there were already a bunch of other androids besides them who were in the know about Project Gestalt and its failure, so were all of these androids living in locations hidden from the Replicants ?

[Protoman]

1 - No, the alien invasion only happens on Year 5012, while Nier Replicant happens on 3366/3470 (depends on version). What is inside that tree is Sleeping Beauty, a server containing the collective memory of mankind. When a Replicant needs to be created, the system will pull out the recollection of a human that lived back then.

2 - They all died off. The Shadowlord was the lynchpin of the Gestalt Project. Without him, the Gestalts can't remain self-aware, and will relapse and die. The project actually succeeded in small settlements (Devola and Popola convinced the Replicants to fuse with their Gestalts), but their numbers weren't enough to keep the population up. In the end, everything died, except androids.

3 - Yes. There is a Devola and Popola in every major human settlement, and they're the caretakers of the Replicants.

One piece of lore that may help you understand the relationship between Nier Replicant and Nier Automata better is this: the YorHa androids are different from traditional androids. YorHa androids were created only a few years before Nier Automata, while the traditional androids existed for thousands of years. Only YorHa androids have black boxes.

This is speculation on my part, but I believe you've switched cause and consequence. The twins inside the tree aren't indicative that the machines were already there on Earth back then, but that the machine network (used extensively in Automata) was copied from this server. Remember the machines didn't always have that form from Nier Automata, they evolved for thousands of years until reaching that. So it isn't a stretch to think they just copied the AIs from inside Sleeping Beauty to build their machine network.

[Cyber Von Cyberus]

Oh yeah, I definitely got misled by how similar Sleeping Beauty was to the network, but didn't remember the years.