Yukiteru Amano is a loner who spends his time writing in his mobile diary and talking to an imaginary friend, Deus Ex Machina. However, one morning, he finds his diary entry for the day has been filled in already. Stranger yet, the events portrayed in the diary start coming true. Deus, who reveals he is an actual God, warns Yukiteru that if he loses his diary, he will die. As Yukiteru starts using the diary to his advantage, he is approached by a stalker named Yuno Gasai who also possesses a Future Diary that foretold his death at the hands of a serial killer, another Future Diary owner. Helping him evade the killer, Yuno helps Yukiteru throw a dart into the killer's phone, killing him. Afterwards, Deus explains the rules of the survival game to Yukiteru and the other diary owners, in which they must try to kill each other in order to win the right to succeed him.

Deus calls a meeting of the eight surviving diary holders, one of whom requests to transfer his diary's ownership. Two weeks after Reisuke's disappearance, Yuki and Yuno transfer to a new school, while a series of brutal murders has been terrorizing the area. After school, Yuki and Yuno sneak in one of the crime scenes with Yuki's classmates Hinata, Mao and Kousaka. When Hinata wanders off, Yuki's diary predicts her being attacked. Yuki rushes everyone to the scene, where they find Hinata's body before a pack of vicious dogs. A strange boy called Aru Akise appears and leads everyone to a nearby building. Aru explains that he's one of Yuki's classmates and that he has been investigating the strange events in which Yuki keeps getting involved. Despite Yuno's mistrust in everyone, Yuki decides to reveal the existence of his diary in order to defend the group against the pack's attacks. After the dogs suddenly retreat, Mao takes Yuki's diary at knifepoint and hands it to Hinata, who is alive and well. Hinata reveals she is the holder of the Breeder Diary and that her real target is Aru, whom she reveals as another diary owner.