Nier: Automata Ver1.1a

YoRHa android soldier 2B is sent on a mission to destroy a Goliath-class Machine lifeform. However, the rest of her unit is destroyed en route, leaving her the sole survivor. Landing at an abandoned factory, 2B fights her way through multiple machines before meeting with 9S, another android specializing in reconnaissance and electronic warfare. They both scout the factory searching for the Goliath until it activates as a massive, building sized Machine. 9S attempts to hack the Goliath but is severely damaged in the process. Angered, 2B destroys the Goliath but is left stranded on top of its remains with 9S as they are surrounded by three more Goliaths. Realizing there is no chance for escape, 2B and 9S self destruct their black boxes, destroying the Goliaths and the factory along with themselves. Some time later, 2B is revived in a new body at the Bunker, YoRHa's orbital headquarters, with her data having been backed up right before her destruction. She reunites with 9S, and finds out to her dismay that 9S prioritized backing up her data first, so he has lost all of his memories shortly after they first met.

The Council of Humanity addresses YoRHa with a speech explaining that Aliens invaded Earth with an army of Machine Lifeforms in the year 5012, forcing what remains of Humanity to retreat to the Moon and build an army of androids in the form of the Resistance on Earth and YoRHa in space with the intention of retaking the planet. Meanwhile on Earth, a Machine designated PLAO8 begins to develop intelligence and instead of attacking the Resistance, decides to learn to grow flowers. 2B and 9S are assigned to head to Earth to investigate why YoRHa's liaison with the Resistance has gone silent. The Resistance sends a team led by the fighter Lily to recover supplies, only for them to be ambushed by an army of Machines. Lily and her surviving team lure the Machines onto a booby trapped bridge while PLAO8 tries to stop from trampling its flowers. 2B and 9S then arrive and destroy the bridge and the Machines, with PLAO8 being destroyed in the crossfire. Elsewhere, more Machines begin reading old books left behind by Humanity as an ominous cocoon like structure is being built.

2B and 9S are guided to the Resistance Camp, where Lily reveals she is the overall leader of the Resistance. At the Bunker, it is revealed that 2B and 9S weren't sent to Earth to assist the Resistance, but to investigate mysterious behavior by the Machines, and YoRHa intends to use the Resistance as sacrificial pawns. Back on Earth, 2B and 9S mean another Resistance fighter, Jackass, who tells them about strangely behaving Machines in the nearby desert. 2B and 9S have Jackass guide them to the desert, where they are ambushed by a Machine patrol. 9S hacks one of the Machines and witnesses a vision of an ancient desert civilization that the Machines were copying. 2B destroys the Machines, and the group pursues another Machine that has decided to flee. Along the way, they discover the corpse of the YoRHa liaison, as well as a mysterious jamming signal. 2B and 9S trace the signal but accidentally fall into an underground chamber where they find a massive cocoon built out of Machine bodies. The cocoon then ejects a human-like Machine which the androids swiftly kill to stop it from evolving, but a second human-like Machine emerges from the corpse and attacks the pair, causing the chamber to collapse.