Once upon a time, an unidentified enemy, the Unknown, suddenly appeared. The "Super Evolutionary Railway Development Agency," had developed the "Shinkalion," a robot that transforms into a bullet train, as a countermeasure against this threat.

The second season of NieR:Automata Ver1.1a. The year 11954. YoRHa Soldiers 2B and 9S are newly dispatched to Earth to carry out and support the 243rd Descent Operation. There, they succeed in destroying the machine lifeform core units, Adam and Eve. With the annihilation of these enemies, the Army of Humanity takes this chance to end this long-lasting war and decides on an all-out attack against the machine lifeforms. This is a record of the battles and hopes of Androids and the fate which dictates them all… As war rages on, Unit 2B and others like her question their role. Reclaiming the planet will take sacrifice, but how much more can they give and is humanity worth the cost?