Just beat the game. What a masterpiece in storytelling. I'm legitimately sad it's over.
I'm still kinda confused with the story, even after hours of reading about it in the mystery files and internet lol. But I think I'm close to getting it.
Someone please correct me if I'm wrong, but I understand the story as this
So. In the late 2100s, humanity developed nanomachine tech. The tech got on the black market, the tech was faulty, the tech essentially wiped out humanity. 15 great minds survived and fled to a space colony.
There, they made a plan to revive humanity, project ark. Project arc would send probes out that were capable of A, producing the kaiju that would terraform compatible planets and B, host the clones of the 15 survivors. Countless probes were sent throughout the universe, to increase the chances of project ark being successful. While at the same time, leading to the possibility of infinite planets being terraformed and inhabited by the 15 clones. Infinite outcomes.
Project arc would have the clones go through a shared simulation, like the matrix, which they would stay in until they were 18, and then they'd be released into the newly terraformed planet with the knowledge of how to be human, through the events they experienced in the simulation.
But Shinonome (2188) became disgruntled with the actions of her co-survivors/humanity as a whole and sabotaged the project. She inserted the deimos code, which would lead to the destruction of the simulation, and the clones in real life. After this, the pods would regrow new clones, and start the simulation again, the "loop"
Clones who became semi aware of the truth, were able to escape to sector 0 before the next loop started. By doing so, they'd be able to grow into adulthood and live in the next loop. Ida and Ms Morimura did this. But by escaping to sector 0, their bodies in real life, on the pod would still be destroyed, but they'd be able to still exist within the simulation as a human AI essentially.
Our main characters beat the kaiju by making the simulation aware of the kaiju. Being aware of this, the simulation awakes them in real life, avoiding another loop. Thus, they are able to beat the simulation, and make it to the real world, where they start to rebuild.
The clones from previous loops, who became AI (BJ, Ida, 426, Professor Morimura) are essentially saved because our clones restart the loop to right before when the kaiju attacked. I think.
Where I'm real confused at, is with everything else lol
So, 426 figures some of this out in the previous loop, and escapes it, to the next loop, to influence events to make the new loop successful?
Morimura, also escaped from a previous loop, loses faith in the sentinels defeating the kaiju, so she wants to activate Aegis. Aegis will destroy the kaiju, but stop the loop process. Thus leading to everyone surviving, but living in a destroyed world?
Then I'm also confused about the construction of the sentinels. Okino says he designed them. Were they only in this loop? Or were the sentinels inserted in every loop/pod, to be created by Okino?