The game begins as Nilin (Kezia Burrows), an Errorist imprisoned in the Bastille Fortress, is having almost all her memory wipedby Memorise. As she is taken to have the last of her memories wiped, a mysterious man called Edge, leader of the Errorists and a man she only hears over her coms device, helps her escape. As she makes her escape through the sewers in an empty coffin, Edge tells her that she is an Errorist with the gift of both stealing and remixing memories. Edge is determined to bring down the new-age aristocracy and bring down Memorise. After escaping into Slum 404, a half-flooded slum district of Neo-Paris, Nilin encounters Tommy, an old friend and fellow Errorist whose memory was completely erased in the Bastille. After retrieving her combat clothes, Tommy and Nilin are attacked by Olga Sedova, a bounty hunter chasing Nilin, planning to use the money to finance a crucial operation for her husband, who has begun to transform into a leaper. Nilin dives into Olga’s mind and remixes her memory so that the first part of her husband’s treatment disastrously wrong and he was retired by the man in charge. Olga then becomes an Errorist ally and transports Nilin to her first destination.
Arriving in the Saint-Michel district, Nilin is told by Edge to steal secret codes from Kaori Sheridan, Neo-Paris’ top architect, aided by another Errorist codenamed Bad Request. After retrieving the codes and uploading them to Edge, Nilin is confronted by Kid Xmas, a strong-arm man from Memorise. They fight and Nilin defeats him, finishing him off with a memory overload. After this, Edge uses the codes to open the Saint-Michel dam, flooding the district and causing damage and death. Though this action makes Nilin doubt Edge’s cause, she decides to continue with the Errorists, this time going through the drained Slum 404 into the Bastille, where the inmate’s memories are stored away for the duration of their sentence. Her goal: to free the stored memories of herself and the inmates, who now include Bad Request, while taking down Madame, the sadistic manager of the Bastille. After retrieving the needed memories from a leaper called Johnny Greenteeth, she makes her way into the Bastille, seeing Memorise scientist Doctor Quaid, then fighting and defeating Seargent Vaughn, a brutal prison guard. Along the way, she tries to free Bad Request from one of Madame’s dark games: she fails and Bad Request is transported elsewhere. Finally, she reaches the memory servers, where the inmate memories are stored, and takes on Madame. After defeating Madame, Nilin releases the memories of the inmates and regains some of her own, though the rest were taken to another location. From her regained memories, she remembers the crime that landed her in the Bastille; on a mission, Nilin infiltrated the mind of a man and made him believe he had killed his wife. The altered memory drove him to shoot himself.
Now partially afraid of what she might discover and unsettled by Edge’s jubilation, Nilin reluctantly goes along with Edge’s next plan: to remix the CEO of Memorise, Scylla Cartier-Wells, to make her see the harm her company’s technology is causing. Memorise is currently working on the Reconversion Project, seemingly a program to rehabilitate both Leapers and criminals and return them to society: but the project is being subverted to control the population. After stealing the needed access codes from Captain Trace, a high-ranking Memorise soldier, Nilin makes her way into Scylla’s office and enters her memory, remixing the memory of a car crash which left her with an artificial leg and a bitterness against the world. As she changes the memory to remove her bitterness, Nilin finds out that she is Scylla’s daughter. With Scylla now restored to a more compassionate person, Nilin is told by Edge to head for the Bastille Basements, relatively undamaged by the prison riot, and both save Bad Request and put a stop to the Reconversion Project. She finds Bad Request, but to her horror his memory has been fully wiped and replaced. As she explores, Nilin finds out that Quaid, who was originally trying to find out the origin of the Leapers, is injecting his own memories into Leapers controlled by their Sensens to create his own private army. Making her way to Quaid, she fights through his private soldiers, but encounters Johnny Greenteeth again, who is revealed to be a former co-worker of Quaid’s who was experimented on and turned into his current Leaper form. The now-insane Johnny kills Quaid, then prepares to blow up the Bastille with himself and Nilin inside. Nilin and Johnny fight, and Nilin is nearly overpowered, but Bad Request attacks Johnny. Bad Request is killed, but Nilin manages to take down Johnny and leaves him inside the facility to die.
With all Memorise’s secret operations taken down and the public up in arms, Edge presses Nilin to find the Conception Cube, Memorise’s central base, and destroy H3O, the Memorise Central Server. Once there, she encounters her father, Charles Cartier-Wells, the creator of the Sensen. Upon finding him, she sees that, fulled by the accident that injured his wife, he has become lost in a dream of an ideal world free from painful memories, all inspired by the desire to help Nilin forget about the accident. Nilin goes into his memory and makes him see the harm his technology causes. Scylla arrives then and convinces Charles to help Nilin enter the Central Server. Once in the presence of the Central Server, Nilin reveals to Edge what she has figured out from his recent talk and his overall strategy: Edge is a an entity created by the amalgamation of unwanted memories within H3O, becoming both Memorise’s greatest asset and its deadliest enemy. Nilin, who unwittingly started Edge with her own memories in her childhood, enters the Server and does battle with H3O/Edge. Though she has come to consider Edge a friend, she destroys him and releases his memories back into the general population. As the memories are released, Nilin remembers Edge’s words about the mind being a fortress, and says that Edge died to remind people that memories should not become open to all, and that painful memories should be lived with rather than forcibly removed. She finishes that outside her now-restored “fortress”, she has a family again, and a damaged world to heal.