Be forewarned: this page contains unmarked spoilers.
One day, YoRHa Unit 2, Type B, heads into battle against a goliath-type machine. She is joined along the way by YoRHA Unit 9, Type S. Together, the two manage to fell the goliath, but at great cost; 9S is severely damaged, and just as they kill the goliath, several more emerge and surround them. With no alternative, 2B and 9S resolve to take out all of the goliaths by setting their black boxes, the cores of their beings, to self-destruct. In so doing, they create a powerful explosion that destroys the goliaths, and themselves as well.
2B awakens in her quarters afterwards on the Bunker, the floating space station used as YoRHA's base of operations. Her memories and personality had been uploaded to a new body moments before her suicide attack. 9S, likewise, had his memories uploaded to a new body, but his personality had been reset.
Together, they receive new orders from their Commander; head to the Resistance Camp in the city ruins on Earth and rendezvous with the leader of the Resistance.
One machine begins to run for its life. 2B and 9S give chase, eventually leading them to a commune of machines attempting various human activities, such as eating, child-rearing, and having sex. When the machines notice the androids, they mount a fierce and desperate resistance, all the while chanting: "This cannot continue".
Eventually, the machines come together and form a sphere, from which emerges a naked humanoid figure called "Adam". 2B and 9S are perplexed by this strange human-like machine at first before fighting it. During the battle, Adam learns the androids' fighting styles and countering them. In the end, however, 2B and 9S manage to subdue Adam, wounding and incapacitating him.
From Adam's wounds emerges another humanoid machine, "Eve", who picks up his wounded brother and emits a bestial cry that causes nearby buildings to collapse, forcing 2B and 9S into retreat.
2B and 9S's investigation leads them to a theater in the park, where they come face-to-face with the machine responsible for the missing YoRHa soldiers; a large machine dressed like an opera singer, whose clothes are adorned with the barely-functioning bodies of androids. The machine speaks of becoming beautiful, devouring androids and machines alike and learning about dressing, accessorizing, and singing; all in an effort to gaining the affections of another machine.
2B and 9S fight the machine and destroy it. Unfortunately, nothing can be done for the androids; they were kept functioning merely to act as weapons for the machine, and with the machine destroyed, are now dead.
As they leave the park, 2B and 9S are approached by a machine waving a white flag, offering to guide them back to its village. The two follow the machine and come upon a village of machines that have adopted a pacifistic lifestyle, led by one machine named Pascal. In truth, Pascal had been cooperating with the Resistance Camp, the two settlements exchanging parts and information in a mutually beneficial relationship.
2B and 9S enter the sinkhole and gain entrance into a mothership used by the aliens. The aliens inside, however, are long dead. The two are approached by Adam and Eve, who, themselves, are physical representations of the machine lifeform network. Adam reveals that he and Eve were responsible for killing the aliens. They had also gained a keen interest in humanity and its complex, contradictory nature, and ask for 2B's aid in helping them get to the humans' moon base. 2B refuses, and Adam resolves to kill her. Before 2B and 9S can defeat them, however, Adam and Eve retreat.
Hundreds of years ago, a machine led others in the foundation of a "kingdom" in the forest, reasoning that a "kingdom" was like a big family. Other machines flocked to the kingdom and gave the "king" their undying loyalty. After some time, however, the king died. The other machines transferred all of the king's data into another machine, one that was infantile in appearance, and resolved to raise the child to maturity so he may become the next king of the forest. Unfortunately, machines do not grow or mature in the same way as humans, leaving the machines perplexed. Nevertheless, they resolved to protect their king forever and ever...
2B and 9S infiltrate the castle and come across the infant "king". Moments after finding the king, however, another android suddenly appears and runs her sword through the "king", killing it in one fell strike. The android is A2, a wanted traitor responsible for killing several YoRHa soldiers and marked for death. 2B and 9S fight A2 to a standstill, with A2 leaving the battlefield, but not before warning them that YoRHa command had betrayed them.
After the fight, 2B and 9S search for more information about A2. The Commander is evasive about why she is a traitor, and Pascal has little information to give, leaving A2 an enigma...
With a powerful electromagnetic barrier rendering the weapons on flight units and satellite laser bombardment useless, 2B and 9S make use of a shore-side artillery cannon to fight it. With even the artillery ineffective, 9S employs one last Hail Mary; commandeering a ballistic missile nearby and flying it into the machine's mouth. The plan works and the machine is destroyed, but the massive explosion causes 2B and 9S to be separated...
Inside the city, 2B finds 9S, who is being held prisoner by Adam. As Adam probes 9S's memories and exposes his weaknesses and insecurities, he explains to 2B that what he is most interested in with regards to humanity is its capacity for hatred. With 2B's hatred laid bare due to Adam's torture of 9S, Adam engages her in combat, going as far as to disconnect himself from the machine network and put his life on the line so he could also experience death.
In the end, 2B slays Adam, then rescues 9S and returns to the Bunker.
The religion the machines had formed was more akin to a cult, as 2B and Pascal learn to their horror; the priest they meet, along with his flock, speak of "becoming as gods", and they believe they can achieve godhood through death. That is, the deaths of all others and themselves.
2B fights a desperate battle through the factory as the cultist machines try to kill her. Along the way, she is aided by 9S, who hacks into machines in the factory from the Bunker to help her escape.
Before aiding 2B, 9S, worried that he may have been infected with a logic virus, performs an overhaul of his memory banks. While performing the overhaul, 9S travels into the central server of the Bunker to investigate strange informational noise. He encounters a strangely high level of security while investigating the server, and eventually happens upon some startling surprises. The first is that many of the containers sent to the humans' moon base are empty, more than one would think for a large lunar colony. The other is records detailing the formation of the Council of Humanity as a part of YoRHa, rather than YoRHa being formed as part of the Council!
After helping 2B escape from the factory, 9S is confronted by the Commander about his discoveries. She confirms his suspicions; humanity is long extinct! The transmissions received from the moon are simply dummy transmissions.
The Commander gives 9S a memory chip, detailing the specifics of Project YoRHa: a project to boost morale of the androids fighting on earth by providing the illusion that humanity still lives on the moon.
After disposing of the goliath, a distress signal comes from Pascal's village; machines are trying to enter the village. After fending off the machines near the village, 2B and 9S are approached by Eve. Driven by grief and rage at the death of his brother Adam, Eve is determined to destroy everything. 2B and 9S fight a fierce battle against Eve, with 9S hacking into Eve to prevent him from recovering from the damage 2B inflicts upon him.
Ultimately, Eve dies by 2B's hand. Unfortunately, in hacking Eve, 9S became infected with a logic virus. Unable to upload his data to the Bunker for fear of spreading the virus, 9S asks 2B to put him out of his misery. 2B reluctantly and tearfully obliges, choking 9S to death and bemoaning "It will always end like this..."
Afterwards, nearby machines blink their eyes, with one coming to life: it is actually 9S, who uploaded his data to the now vacant machine network, thus preserving his memories and personality!
2B and 9S participate in the assault and square off against the myriad machine forces in the city ruins, who fight back relentlessly. They help out various squadrons battling the machines, but are soon struck by a powerful EMP blast. When they come to, they find the other soldiers writhing in pain before their gazes turn to 2B and 9S, and their eyes give off a menacing crimson glow...
The YoRHa soldiers on earth have become infected with a logic virus, and turn their blades against 2B and 9S. With the operation compromised, communications with the Bunker cut off, and surrounded on all sides by infected soldiers, 2B and 9S set their black boxes to self-destruct. In so doing, their consciousnesses are transferred to new bodies on the Bunker, and they relay what they witnessed to the Commander. The Commander, however, finds their claims dubious and orders them detained for suspicion of viral contamination.
Before the soldiers on the Bunker can detain 2B and 9S, however, they also succumb to the logic virus and attack them. 2B, 9S, and the Commander make for the hangar, but before they can escape, the Commander becomes infected. She orders 2B and 9S to escape without her while she stays behind on the Bunker, and the two retreat to Earth as the Bunker self-destructs.
2B and 9S become separated as they make their escape. Eventually, the machines converge on 2B and force her to crash-land in the flooded city. To make matters worse, the logic virus has infected her as well. Determined to prevent other androids in the area from becoming infected, she makes for the shopping center, an area far away from other androids.
Just as she arrives at the shopping center, her body and mind ravaged by the logic virus, two infected soldiers assail her. As it seems all hope is lost, A2 appears and slays the infected soldiers. At the end of her rope, she begs a boon of A2...
9S lands not far from the shopping center and follows 2B's black box signal, only to see her moments after she is run through on A2's blade. Overcome with rage, 9S charges at A2, only for them to be separated by a sudden burst of seismic activity that causes a strange tower to appear from beneath the city ruins...
In the desert, A2 crosses path with a massive and powerful goliath. With the goliath proving to be overwhelmingly powerful, A2 engages "B-mode", an ability unique to older models of androids that increases her strength severalfold, but risks damage to her systems. In the end, she destroys the goliath, but the toll of having the machine's memories merge with hers while hacking it, on top of 2B's memories being part of hers, causes her to pass out.
Determined to destroy the machines and kill A2, 9S makes his way to the first resource recovery unit in the forest, labeled "Meat Box" in an arcane language. The inside of the unit is brimming with machines that 9S slaughters as he fights his way to the top, destroying the machine core and gaining his first key.
At the village, A2 agrees to help Pascal around the village to pay him back for providing her with a new filter, learning more about the machines of the village and beginning to develop a sense of companionship with them.
When A2 returns to the village with supplies Pascal requested, however, she finds the village in flames. Following a bizarre sound, many of the villagers went berserk and started eating one another. A2 destroys the berserk machines, but aside from Pascal and some machine children, everyone in the village perishes.
Pascal escorts the children to the abandoned factory that was once home to the machine cultists. Unfortunately, they are not safe here either; vicious machines converge on the factory. A2 fights them off in an effort to protect the children, and Pascal casts aside his pacifist beliefs to commandeer the hulk of an inactive goliath to destroy the invading machines.
When A2 and Pascal return to the factory after driving off the invaders, however, they come across a horrific sight; the machine children had taken their own lives. Pascal feels responsible for their deaths; he had taught the children "fear" to foster in them a sense of caution that would help them stay alive, but that very same fear drove them to end their own suffering.
Overwhelmed with grief and sadness, Pascal asks A2 to end his torment, either by taking his life or deleting his memories...
After leaving the unit, 9S suffers a malfunction that renders him unable to use his weapons. He makes his way back to the Resistance Camp, where Devola and Popola repair him. The twins are worried about 9S's decline, but 9S is deaf to all reason at this point...
Within the tower, 9S is confronted by a group of 2B-model androids. Insane from his ordeals, 9S relishes the chance to destroy the 2B androids, only for the last android he fells to self-destruct...
Meanwhile, A2 learns that the tower is open and makes her way there. Inside, she discovers a massive library with details related to Project Gestalt and a patient named "Yonah"...
9S awakens and discovers his left arm had been destroyed by the explosion of a 2B model. He rips the arm off of a nearby 2B model's body and attaches it to his body, then continues his ascent up the tower. He encounters a pair of girls dressed in red, speaking in a bizarrely deep voice, granting him a "reward": the truth about the disposal of YoRHa. The Bunker had been designed with a backdoor that would open, facilitating the mass infection of all current YoRHa androids with a logic virus in order to wipe them out and clear the way for new models. 9S and everyone he ever knew, everyone he ever cherished, were considered utterly disposable...
Back at the library, A2 is attacked by a multi-legged goliath. During the fight, she is hacked by the girls dressed in red and forced to fight them. With the help of Pod 042, however, she discovers a weakness in the artificial intelligence of her assailants; by not destroying the enemies that appeared before her, she could let the red girls continue to multiply their consciousnesses until they began to fragment. Once the fragmentation occurs, the girls in red would fight among and destroy themselves.
The two continue their ascent up the tower, fighting their way past swarms of machine lifeforms, and finally meet one last time at the very top. 9S, disillusioned, vengeful, and corrupted by the logic virus, has decided that he would kill A2, destroy the machine lifeforms, then use the tower to destroy the lunar server. A2, however, carries 2B's memories and will in her. She reveals to 9S that 2B's true designation was "2E": YoRHa Unit 2, Type "Executioner". Because 9S's curiosity and inquisitive nature made him very likely to discover the true nature of YoRHa, 2E was tasked with killing 9S whenever he came too close to the truth. A2 believes that 9S may have known this truth all along, but hearing it from A2 only infuriates 9S.
The two reach an impasse, and come to blows in a battle that results in the loss of both of their lives.
Pod 042 starts a data salvage to preserve the memories. A system purge is initiated in response, and Pod 143 warns 042 that they risk their consciousness data being lost. 042, however, refuses to heed the warning and, through the player's control, struggles to prevent the loss of his memories.
The defense program carrying out the purge suppresses the player, impeding their progress. With each failure, however, messages of encouragement from other players who performed the ultimate sacrifice to help others in need come through. Eventually, one player comes to their aid, helping them complete the data salvage.
With their memories saved, Pods 042 and 153, along with other Pods, set to work rebuilding 2B, 9S, and A2. There is a possibility that, as a result of being remade exactly as they were, the same result will occur. Pod 042, however, believes in the possibility of a new future for them...
