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.

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.

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.

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.