As the machine war progresses, YoRHa Command and the Resistance prepare for a final decisive assault against the "Machine Lifeforms," the militarized robots who roam the earth's surface. While preparations are underway, YoRHa 9-gou S-gata "9S" and YoRHa 2-gou B-gata "2B" continue their advanced scouting mission. However, 9S and 2B struggle with their respective roles, their loyalty to each other, and their loyalty toward Command.

Although the nefarious Adam and Eve have been defeated, it appears the machines are not down for the count. An ominous presence in the form of the "Red Girl" continues to observe the androids from afar, waiting for the perfect opportunity to attack them.