Yukiteru Amano is a shy middle schooler who regularly keeps track of what he does in his daily life by writing down all of his activities on his phone—a digital diary. Despite having no friends at school, Yukiteru is frequently seen talking to his supposedly imaginary friends Deus Ex Machina, the god of time and space; and Deus' servant, Mur Mur.

One day, Yukiteru wakes up and discovers that certain events of his day are preemptively displayed on his cellphone. While initially dismissing it as a coincidence, he slowly realizes that the incidents written in his phone actually take place in the near future. After spending the day benefiting from this new asset, Yukiteru learns that his classmate Yuno Gasai possesses a similar diary.

As the two team up to defeat an odd pursuer and head back to their respective homes, Deus Ex Machina explains that they—alongside 10 other contestants—have been drawn into a survival game whose victor will become the deity's successor. With no other options, Yukiteru and Yuno must use their cellphones—now called "Future Diaries"—to survive this unforgiving battle royale.