Warning: This article contains major spoilers for the story of NieR: Automata and the fate of the Replicants.
The Replicants were new bodies created through Project Gestalt back in the original NieR. In NieR: Automata, we are told that the last remaining humans actually flew to the moon after aliens invaded Earth. This suggests that Project Gestalt must have been a success, and the Gestalts were able to fuse with the Replicants in the end. However, this couldn’t be further from the truth.
As we play through the game for the second time as 9S, you find out that Project Gestalt was actually a failure after Devola and Popola were unable to protect the Shadowlord. The Project crumbled, and all the Devola and Popola android models gathered the Replicant data and sent it off to the moon as a beacon. This later became the data relay point that transmitted the human propaganda messages the YoRHa androids constantly received.
To prevent the androids from falling into severe depression and losing all sense of purpose, which would ultimately lead to their extinction, a higher chain of android command decided to launch Project YoRHa. New combat androids would be created to aid in the war against the machines, but before the androids could actually push them back, a backdoor in the androids’ Bunker would be opened, and they would all be infected and destroyed by a logic virus. This was done so that the machines would never be completely destroyed, the war would never end, and new androids would be manufactured to continue fighting, all so that they never lose their sense of purpose.
Long story short: Replicants are all dead, and humanity is a lie.
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