The story begins during an initial invasion where androids 2B and 9S serve the Resistance under the leadership of Anemone. While clearing out machine threats, they make the startling discovery that their enemies are actually exploring human concepts and building their own societies. They eventually cooperate with a peaceful machine named Pascal and confront Adam and Eve who serve as the physical manifestations of the entire machine network. During these missions, they also cross paths with a rogue android named A2 who is currently fleeing from YoRHa.
A dark truth emerges after 2B kills Adam because 9S finds a glitch in the servers during a data sync. He learns that humanity has been extinct for a long time and the Moon server is merely a propaganda tool designed to maintain android morale. When Eve goes insane with grief over his brother, 2B and 9S are forced to destroy him to end the chaos. Although 2B is forced to kill 9S to stop a virus infection, his consciousness manages to survive within the local network.
The final act starts with a full scale YoRHa invasion that turns into a disaster. A logic virus attack corrupts almost every unit except for 2B and the newly restored 9S. After they are separated, 2B becomes infected and chooses to upload her memories into her sword before asking A2 to watch over 9S. Unfortunately, 9S witnesses A2 killing 2B without knowing the mercy behind the act and he vows to get revenge. As a giant machine Tower rises from the ground, A2 learns to empathize with her enemies while 9S descends into madness. With the ultimate sacrifice of Devola and Popola, the gates to the Tower finally open for the final confrontation.
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