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.

The Machines are shown gaining more intelligence as they increasingly mimic human behavior. At the Resistance camp, 2B and 9S debrief Lily and Jackass on the human-like Machines they encountered, which YoRHa has dubbed "Adam" and "Eve". Jackass muses on the possibility of making peace with the Machines, but 9S flatly rejects the idea. 2B and 9S are then ordered to scout a nearby amusement park to investigate the disappearance of an android soldier. To their surprise, they find the Machines there are not hostile, and advance into a theater. There, they encounter an advanced Machine called the Songstress which attacks them on sight. 9S attempts to hack the Songstress and manages to catch a glimpse of her memories, where she fell in love with another Machine, who ignored her, and became obsessed with making herself look beautiful, turning her into the monstrous machine she is now. 2B manages to expose the Songstress' core and destroy her. 9S coldly declares Machines can't feel emotions and then destroys a pair of nonviolent Machines, much to 2B's concern.

Adam and Eve are shown steadily gaining intelligence as Adam eagerly reads old human books. 2B and 9S are given a mission by Lily to deliver supplies to a village of Machine lifeforms that have developed into a peaceful community and are willing to trade with the Resistance. They head to the village and meets its leader, Pascal, who explains that he and the other Machines in the village have severed themselves from the Machine network and now live peaceful lives. 2B and 9S are intrigued at how the Machines have been able to form a functional, human-like society. They then explore an underground chamber beneath the village, where they find an Emil head. 9S tries to hack it and catches brief glimpses of Emil's memories, and deduces the Emil head is one of many robotic weapons developed by humans to fight the Machines. Pascal explains that the village revere the Emil head, as it was what triggered their desire for self preservation and peace. However, 9S remains conflicted at the idea that Machines can grow beyond their programming. Meanwhile, Adam and Even continue to gain more knowledge, and Adam convinces Eve to refer to him as the older brother.

2B, 9S, and Lily head out to set up a Machine early detection network. While 9S heads off to troubleshoot the system, Lily tells 2B about how the Resistance first met YoRHa. After a botched landing operation only left four YoRHa androids alive, led by a No. 2 model similar to 2B, they appealed to the Resistance for assistance. The Resistance, who weren't aware of YoRHA's existence at the time, mistrusted them, but their leader Rose agreed to work together. The combined group then headed for the location of a Machine server to destroy it. Along the way, Lily was infected by a Machine logic virus, which the Resistance had no way of curing. No. 2 intervened and convinced the team to subdue Lily instead and the YoRHA squad used a vaccine to cure her. The team then continued on to the server, only to be attacked by a massive Machine army. While the server was successfully destroyed, shutting down the Machines in the area, Lily was left as the sole survivor, leaving her bitter against YoRHa for refusing to send reinforcements. 2B then asks Lily if there is the possibility that any of the team survived the mission, but Lily expresses doubt. Elsewhere, it is revealed that No. 2 is still alive and fighting Machines on her own.

Adam and Eve continue to accrue knowledge until Adam decides to visit the "Playground". Meanwhile, 2B and 9S remain on standby as they haven't been given new orders yet. Pascal then approaches them, asking them to help save a missing villager who wandered into the Forest Kingdom, a nation of similarly independent but highly hostile Machines. 2B and 9S agree to investigate and travel to the Forest Kingdom with Pascal, where they find all of its inhabitants massacred by an unknown assailant. Exploring the castle more, the group learns that the Forest Kingdom's original king had died over a century ago, and his followers carried on his legacy by transferring his memories into an infant machine which they protect to this day. They are able find the missing villager who was hiding with a surviving Forest Kingdom soldier, and the two of them have decided to marry, confusing 9S. The group then heads to the infant Forest King, but are too late to prevent it from being killed by No. 2, now identified as the fugitive android A2. 2B and A2 briefly clash until A2's sword breaks and she decides to withdraw. 9S asks A2 why she would betray YoRHa, but A2 retorts that it was YoRHa that betrayed her before taking her leave.

The Commander tasks 2B and 9S to track down and eliminate A2, but won't tell them what caused her to betray YoRHa. They try to gain more information by questioning the Resistance members. Lily recognizes A2 as No. 2, but hides that fact from 2B and 9S, instead telling them she has no idea where A2 is. The pair then head for the coastal ruins to find Jackass. After a brief discussion on human behaviors often considered unnecessary, 2B finds a Lunar Tear flower and wears it on her chest at Operator 6O's suggestion. 2B and 9S then split up. 2B finds Jackass fishing and questions her. Jackass reveals she doesn't know anything about A2 other than she used to be No. 2, which 2B has already known. 2B attempts to contact 9S but is concerned when she discovers his signal is jammed. Meanwhile, 9S hacks into the Bunker's system to try and find more information on A2, but is forced to disconnect when his intrusion is discovered. He then pursues what he thinks is A2 until he ends up in a surreal space and is attacked by an unknown entity. Elsewhere, Eve searches for Adam but is shocked when he cannot detect him on the Machine network.