During work at Junk Shop Mediocrity, Aoba Seragaki goes out on a delivery with his Allmate, Ren, and encounters his childhood friend, Koujaku, and his Allmate, Beni. After a short conversation, Aoba makes his delivery to Yoshie and is forced to stay until nightfall. On his way home, Aoba is harassed by members of the Ribstiez group, Bug Bomb, but is saved by his friend and leader of Dry Juice, Mizuki. Mizuki voices his concerns of Ribstiez being overshadowed by the popular cyber game, Rhyme, and tells Aoba of the mysterious disappearances of several Ribstiez groups, rumored to be the works of the mythical group, Morphine. As they part ways, a Rhyme battle soon starts near Aoba and he observes it before meeting up with his old friends, Virus and Trip. The game is soon interrupted by a police officer, Akushima, causing Aoba to hurry back home.

Directly after Aoba's first attack, his normal personality reappears with no memories of what he just did. The mysterious player has his rabbit Allmates relentlessly attack Aoba and Ren again, which causes Aoba's other personality to resurface and seemly destroy the Rhyme Field, ending the battle. Aoba's and Ren's unconscious bodies are safely taken back to Mediocrity by a man wearing a gas mask, who called Aoba "Master". When they awaken, Aoba and Ren both find themselves with no memories of how the battle ended.

The young man silently purchases an item from Aoba, leaving the shop without identifying himself. When returning home from work that evening, Aoba finds the young man in his bedroom, who reveals to Aoba that he was the person in the rabbit costume that forced him in the Rhyme battle. The teenager demands a rematch with Aoba and threatens to destroy Ren if he doesn't. Clear arrives via veranda to Aoba's room, telling the intruder to not hurt his "Master". Koujaku soon joins the group, and a scuffle initiates between him and the teenager. Tae breaks them up and the group settles down in the kitchen, where the young man introduces himself as Noiz. The next day, Aoba and Koujaku visit Mizuki in hopes of cheering him up, as he has been depressed about losing more of his team members to Rhyme.

Tae denies having any connections to Aoba and asks what Takahashi want from her. Inside, Aoba watches a live interview of the owner of the pleasure area Platinum Jail, Toue, and ridicules the man's speech of "perfect happiness". Once Tae enters the house, she lies to Aoba before both of them return to their bedroom. As Aoba muses over his contentment for his current life, he hears singing outside his window and finds Clear on his rooftop. Clear explains the song he was singing is called the "Jellyfish Song" he made up himself and used to sing to his grandfather, who has passed away. When Clear questions Aoba about why humans live the way they do when they are bound to die, Aoba says that humans want to live their lives happily and leave proof of their existence before they do.

Aoba wakes up in Scratch's hideout and quickly suffers a beating from Mink's men on his orders. As Aoba struggles to break free, his other personality briefly takes over and orders the Scratch members to stop before falling unconscious. When Aoba awakens safely in a bedroom with Ren and his bag, Mink states to Aoba that his aware of Aoba's special "voice" and will help him find Tae if Aoba obeys him in return. Although reluctant, Aoba agrees and heads back to his house, meeting up with Clear and Koujaku. Koujaku is distrustful of Mink since his group is made up of criminals, but relents once Aoba explains that Mink will help him find Tae. The group then discovers that Noiz is spying on them and recruits him to their mission. Despite some tension, the group is able to track down Tae's location and Clear guides them to an abandoned warehouse area. They are attack by hooded men, which turns out to be the missing members of Dry Juice.

As Mizuki breaks down, Aoba is pulled into a Rhyme Field and meets Toue. Toue addresses the baffled Aoba with familiarity, and encourages him to discover who he truly is before disappearing. Aoba awakens in the real world, but quickly collapses after spotting an unconscious Mizuki. At Oval Tower, Takahashi reports to Toue about the data they received on Aoba's powers, and that he had sent the police to apprehend him. Later that night at their house, Tae informs Aoba that Mizuki and the rest of Dry Juice were taken to a hospital, but all of them are in a comatose state. She explains that Mizuki was being controlled by Morphine, who works for Toue, and how she was once a neuroplasticity researcher for Toue's labs twenty years ago. Tae quit once she learned that her research was being abused for Toue's brainwashing experiments, but upon her recent refusal to come back to the research labs, Toue used Mizuki to force her to cooperate.

Aoba and Koujaku meet each other at the entrance of Platinum Jail, and the former scolds the latter for going off on his own. Once they enter Platinum Jail, Toue makes a live announcement that a special event will be held for Platinum Jail's 10th anniversary while Aoba notices the crowd's dazed expressions before the announcement is concluded. Later, Koujaku spots a man, Ryuho, entering a club and anxiously chases after him with Aoba following behind. While looking for Koujaku in the crowd, Aoba faints from the club's drug lights and collapses against Ryuho. When Aoba awakens in Ryuho's room, Ryuho reveals to him that he is a tattoo artist and saw Aoba once before, and could sense he was different from others.

While searching for Ren, Aoba finds Noiz in the living room, tinkering with Ren. Furious, Aoba takes Ren away from Noiz aggressively, causing Noiz to accidentally scratch himself with a screwdriver. Aoba notices the injury and apologizes for hurting Noiz. While treating the wound, Aoba receives another download of "Silent Oath", and Noiz attempts to trace the source to the sender but to no avail. Aoba inquires what Noiz is doing in Platinum Jail, promoting the latter to show the former that he also got an invitation. Later, Ren informs Aoba that Noiz simply removed a worm from his system. The next morning, Aoba apologies for snapping at Noiz, who merely brushes it off, claiming that he only did it on a whim because he thought that Ren was the reason Aoba beat him in Rhyme. Noiz asks Aoba why he is being nice to him, and suspects that is trying to gain something from helping him. Before Aoba could respond, Noiz takes off to shop for food and Aoba follows him.

Aoba and an injured Noiz are ambushed by Morphine members when Clear appears and easily defeats them. When one of men tries to hurt Aoba, Clear violently beats the man up until Aoba stops him, allowing the Morphine member the chance to throw acid on Clear and escape. At their lodging, Clear refuses to remove his mask in front of Aoba, explaining his grandfather told him never show his face to anybody because it wasn't "normal" like other humans and is afraid that Aoba will hate him once he saw his face. Aoba assures Clear that he could never hate him and takes off his mask, revealing Clear's normal-looking face. Afterwards, Clear cooks for Aoba when strange music plays on the TV, causing Aoba immense pain. Clear explains that Toue uses the "Dye Music" song to brainwash people. Later, Clear questions Ren why he doesn't call Aoba "Master" even though he is just an Allmate, with Ren saying that he is only doing what Aoba wants from him.

Noiz performs emergency repairs on Clear, but informs Aoba and Koujaku that he is unable to properly fix him. Aoba tells Noiz and Koujaku about his Scrap ability and his suspicion that Toue is planning to use Plantimum Jail's Special Anniversary Event to brainwash the citizens on the island. Aoba is resolved to stop him, but doesn't want Koujaku and the others to be involved, as he fears that it would put them in danger. Later that night, Mink calls Aoba, and the two plan to break into Oval Tower by themselves. Mink hands Aoba an USB flash drive to put into Ren with a program that will disable the security Allmates patrolling the building. Although Aoba vehemently refuses to use it, as it could possibly destroy Ren, the latter assures the former that he is okay with the plan. Aoba and Mink infiltrate Oval Tower's control room and upload the program to its system, and although Ren appears to be fine, Aoba notices he is acting strange.

As Mink and Aoba venture higher up into Oval Tower, Aoba spots specks of light fluttering on Ren's face, but Ren coldly brushes him off. When Mink and Aoba are separated while escaping the guards, Aoba encounters a holographic Sei, who is pleased to finally meet Aoba. Sei explains to the bewildered Aoba that he was one the who sent demos of "Silent Oath" and the invitation to Platinum Jail, guiding him to Oval Tower so Aoba could "break" him with his power. As Sei is at his limit, he encourages Aoba to hurry and come to him before his hologram disappears. Aoba is then captured by Morphine, and learns that Virus and Trip are the leaders of the group. They reveal that they were they ones that erased Aoba's memories of his time playing Rhyme in order to keep him hidden from Toue, as they wanted Aoba to themselves. Additionally, they tell Aoba that Sei is his older twin brother, and both were designer babies created by Toue using Tae's research.

As Ren's memories pour inside Aoba's mind, Aoba uses Scrap on himself in order to speak with him. Aoba sees that Ren is falling apart due to the worm. Ren reveals he was originally a part of Aoba's consciousness, his "restraint" that was created to monitor his "desire" (the other Aoba) so that it wouldn't take control of him. However, there was a period of time when Aoba's "desire" took hold of him and Ren could no longer influence him from inside his mind, prompting him to transfer his consciousness into the Allmate's dog body when Aoba discovered it. As a physical being, Ren was able to influence Aoba more easily, but because of Virus and Trip tampering with Aoba's memory in the past, Ren had forgotten his original purpose until the worm infected him.