Yukiteru Amano is a timid middle school student who habitually records everything he does in his daily life on his phone—a digital diary. At school, he has no friends, but he is often seen talking to his supposed imaginary companions: Deus Ex Machina, the god of time and space, and Deus' servant, Mur Mur.
One morning, Yukiteru wakes up to find that certain events of his day are already appearing on his cellphone ahead of time. At first he dismisses it as coincidence, but he slowly realizes that the incidents written on his phone actually occur in the near future. After benefiting from this new ability throughout the day, he discovers that his classmate Yuno Gasai owns a similar diary.
When the two team up to fend off a strange pursuer and return home, Deus Ex Machina reveals that they—along with ten other participants—have been forced into a survival game where the winner becomes the deity's successor. Left with no other choice, Yukiteru and Yuno must rely on their phones, now called "Future Diaries," to survive this merciless battle royale.