One rainy night, high school student Sakura Sakurakoji sees people being burned alive. At school the next day, she meets new transfer student Rei Ogami, the boy she believes was with the burning people. Sakura then resolves to uncover Rei's involvement.

Sakura wakes up in her own bedroom after being found outside the night before. Fearful of Ogami, she becomes protective of Aoba, who mistakes Sakura's actions for unfriendliness. Sakrura calls Ogami out to get to the bottom of the events in the park.

Ogami is given his next assignment by the Eden council. Toki picks up Sakura to walk to school, claiming that he is Ogami's friend. Ogami catches up, and starts fighting with Toki, but Sakura stops them both. Toki tours Sakura and Ogami's school.

Ogami, Toki, and Sakura attempt to infiltrate a government-run facility, and encounter two large men with their own special abilities. They locate Diet member Tabata, their target, and are about to carry out their mission when a new secret is revealed.

Toki has a breakfast meeting with the Prime Minister. On their way to school, Sakura and Ogami run into Rui Hachioji, who has a message for Ogami. Sakura urges Ogami to open up and befriend the others in their class, but the class has a surpise of its own.

As Ogami lies unconscious, Heike and Kanda fill Sakura in on their Code: Breaker roles. Sakura invites everyone to her house to stay out of danger while Ogami recovers. The remaining Code: Breakers also meet up there, when they get an uninvited visitor.

In the aftermath of Hitomi's visit, Toki runs off by himself, while the others put their heads together to figure out what Hitomi's objective was. For different reasons, both Sakura and her parents reaveal to Ogami how important their family is to them.

The Code: Breakers believe that Hitomi is behind the explosions throughout the city. They receive an anonymous message informing them of Hitomi's location. Ogami rushes to the site hoping to find Sakura there as well, but finds an unexpected surprise.

Hitomi is made a Code: Breaker at 16, and works for the organization for over a decade. As his allies fall in the line of duty, he reminds himself that he is working to create a world where children can laugh. Then a shocking secret is revealed.

The Code: Breaker team discovers where the bombs are planted. There are too many of them to deal with, but between the police, the Kizakura-gumi gang, and Yuki, they do their best to deal with them. Meanwhile, Ogami heads to Sky Tower to confront Hitomi.

Toki arrives at the rooftop where the Prime Minister is being held. Oji and Yukihina fight for the custody of the children with special abilities. Inside Sky Tower, Hitomi fights Ogami to a standstill, and threatens to fulfil his plans to change the world.

Heike is astounded by the full extent of his Ogami's capabilities, as Ogami and Hitomi engage in a final showdown. Hitomi reveals why he had no choice but to carry out his plan, and swears vengeance against the Prime Minister. Sakura says her goodbyes.