While 9S secured an escape route for 2B, he hacked into the machine network and discovered files related to Project Gestalt. This project ended up a massive failure and all of humanity was wiped off the face of Earth. The Replicant data from the project was gathered and fired off to the moon as a beacon. The moon beacon was then used as a relay point to consistently ping messages to Earth and the Bunker to make the androids think that humans were still alive and well.
In order to perpetuate the lie and to keep the surviving androids’ morale from sinking to an all-time low, Project YoRHa was launched. This project sought to train elite androids to help take back the planet from the machines. By lying to the YoRHa units that humanity was still alive, the androids would feel that they still had a purpose and something to fight for as an android’s basic instinct is to serve and protect human beings. Knowing that all humans were dead would inevitably cause the androids to sink into depression, thus leading to their eventual extinction. Only a trusted few were privy to this information, such as the YoRHa commander.
Meanwhile, we see the mental breakdown of Eve due to the death of his twin brother Adam.
Platform: PlayStation 4