Keigo sends Yuki and Yuno to an amusement park to act as bait for Uryu. When Yuki asks Yuno why she keeps following him around, she reminds him of the day they met, one year earlier. Yuki was depressed over his parents’ divorce and, to cheer him up, Yuno offered to marry him in the future. Yuki agreed, thinking it was a joke. Although Yuki realises Yuno’s still hiding something from him, she refuses to divulge anything more. That night, Yuno invites Yuki to stop by her house. While searching for the bathroom, he opens the door to a room containing three decomposed corpses, an act which changes the future of every Future Diary owner drastically. Terrified, Yuki runs home, only to find Yuno right outside his door. Meanwhile, Uryu finds evading the police difficult, despite her diary’s ability to secure escape routes. Exhausted and cornered, she is approached by a mysterious man, who offers to save her and takes her to a hut in the woods. There, he reveals himself as a Future Diary owner, drugging and torturing her to get information on other diary owners.

Minene Uryu, a terrorist and Future Diary owner, holds Yuki’s school hostage, having rigged its corridors with motion sensor bombs. By combining Yuki’s diary’s ability to predict everything happening around him and Yuno’s diary’s ability to predict everything happening to Yuki himself, the two manage to evade danger, until Uryu threatens to detonate all the bombs unless Yuki is handed over to her. Yuki is captured by his classmates, angering Yuno who runs down the corridors, causing several classrooms to explode on purpose. Yuki and Uryu are soon confronted by Keigo Kurusu, a police officer with a Future Diary cell phone that is able to predict crimes. Keigo, Uryu’s true target, reveals he is not interested in the survival game and just wants to stop criminals. Working together, Yuno, Keigo and Yuki’s classmates distract Uryu, allowing Yuki to throw a dart at her Future Diary cell phone. However, Uryu dodges it, injuring her left eye and escaping using her diary’s ability. In the aftermath, Keigo forms an alliance with Yuki and Yuno to stop the other diary owners.

Yuki Amano has few friends and spends most of his time writing in his cell phone diary and speaking with an imaginary friend named “Deus ex Machina,” the God of time and space. One day this god talks back to him, forcing Yuki to participate in a high-stakes game where 11 other people are out to murder him within 90 days. Their only advantages are their cell phone diaries, which aid them in variou ways.