The game begins with a playable flashback segment of the first game where the player leads The Dishwasher through the Grace Chapel, building up to the boss fight against Yuki. The Dishwasher emerges victorious from this battle and Yuki dies in his hands.
It is revealed that after the events of the first game, The Dishwasher and Chef destroyed the world after it became uninhabitable. This crime was pinned on Yuki however, who was witnessed escaping the scene, having mysteriously been reanimated. During her time in the Iffenhaus prison ship she experiences recurring nightmares caused by an entity known as The Creeper, and wakes up to the image of her slaughtering a prison guard. With her newfound powers she breaks out of the prison and stows herself away in an escape pod shortly after getting her arm cut off in battle.
She crashes onto the moon and wakes up, only to find herself with a chainsaw implant where her arm used to be. She then and there decides to pursue a quest for revenge against the three figures of power known as The Banker, General and Judge, all of whom were responsible for her incarceration. During this time The Dishwasher who has relocated himself to the moon finds himself searching for the heart of the new Cyborg movement, following Yuki's blood trail of revenge. The game is broken up into two solo campaigns that largely run in tandem with each other. They break off midway into separate stories once the two protagonists meet each other for the first time, however.
In Yuki's storyline, she finds herself in another hallucination where she finds a knife and uses it to kill who she believes is her manipulator, The Creeper. However she regains conscious and finds out that she inadvertently has stabbed The Dishwasher with it. Yuki becomes distressed but is reassured by him that he's okay with it, as it's only fair she repays him the favor for having killed her once. The Dishwasher rips the knife out of his body and dies. The Creeper then appears before Yuki and is killed by her in a fit of rage and hate. Chef then arrives to the scene, explaining to her that killing The Dishwasher shouldn't be possible as the Chef, Dishwasher and Yuki all share the same inhuman blood that makes them unkillable through normal means. He tells Yuki that the knife she extracted from her nightmares should be taken back and used to murder her inner demon who is driving her to the brink of insanity. Yuki succeeds, and proceeds to kill her final mark, the Judge, who has become a symbiont for The Fallen Engineer. In the end after facing the fact that the world is still in chaos and that her stepbrother is dead, her only care in the world is that she's finally free.
In The Dishwasher's storyline, Chef confronts him, explaining to him that Yuki is being manipulated by The Creeper, who must die if Yuki is to have her freedom. The Dishwasher finds Yuki being manipulated by The Creeper, but quickly kills The Creeper so as to not having to resort to killing Yuki again. Yuki regains conscious and finds The Dishwasher standing over The Creeper's dead body. The two then reconcile, however Yuki remains convinced that her mission for revenge is one that she must carry out alone. The Dishwasher leaves her to her mission, as he continues his search for the source of Cyborgs. He eventually reaches the Judge's tower where Yuki prepares to exact her revenge, however through an accursed mask the Judge manages to act as a symbiont for The Fallen Engineer, the true antagonist of the plot, and he partakes with The Dishwasher and Yuki in a battle. The Engineer manages to enter the depths of The Dishwasher's stagnant nightmare and tries to kill him from the inside. The Dishwasher overpowers him however, and ultimately kills him.
Characters
The Dishwasher – The unnamed protagonist of the series. Once a regular dishwasher at the Foghorn Café, he was murdered in the first game during the Cyborg movement but then revived by the Chef, along with being granted inhuman powers which he used to exact revenge upon the Synthesis AI, responsible for manufacturing the Cyborgs. Since then he has teamed up with Chef and become a silent vigilante. Unlike the first game where he goes on an unstoppable quest for vengeance, The Dishwasher has since become a lot more collected and acquainted with his abilities, and is only determined to use his powers to purge all evil in the universe. His quest on the moon revolves searching for an unknown entity who is controlling all evil behind the scenes. He's very proficient at the electric guitar, and is accompanied by a red-eyed crow throughout the game.
Yuki – The Dishwasher's stepsister who was presumed dead during the first game. After dying in the hands of her stepbrother she is revived by an entity known as The Creeper, granting her powers much like The Dishwasher's, but also letting her become manipulated into trying to kill The Dishwasher, suffering recurrent nightmares and hallucinations involving a hideous demon with an insidious smile. After the first game Yuki had escaped earth during its final hours when The Dishwasher and Chef set it ablaze, destroying all remains of life. She was scapegoated as the earth's destroyer and sentenced to rot in the Iffenhaus Space Prison. After her powers awaken, she breaks out of the prison and goes on a quest for vengeance, much like her stepbrother before her, pursuing the three figures of power responsible for her incarceration; The Banker, General and Judge. She's very proficient at the violin, and is accompanied by a cat with wings throughout the game, whom she has named Paka.
Chef – The Dishwasher's mentor and savior. The Chef of the Foghorn Café is an ominous and inhuman being who claims to have alien blood running through his veins, granting him inhuman power. It is with the same blood that he resurrected The Dishwasher. With the help of The Dishwasher he managed to destroy the world after it got plagued by Cyborgs and undead. Their partnership continues in this game where they are out to kill all evil in the universe through any and all means necessary.
The Banker, General and Judge – The three pillars of power and Yuki's marks of revenge. The Banker, General and Judge are the trifecta of control in the new world. They have since its conception been corrupted with power and run an incredibly fascist and corrupt society on the moon where Cyborgs regulate everything and undead roam the streets, much like the world before it.
The Fallen Engineer – The creator of the Synthesis AI and Cyborgs, The Fallen Engineer is The Dishwasher's nemesis and the main antagonist of the game. He is obsessed with creating a world filled with despair and lies, controlling all schemes from behind the scenes. He's resurrected as a symbiont with the help of an accursed mask and fights the protagonists in the center of their own nightmares.