The story centers around three siblings, twins Kanba and Shouma, and the ill sister, Himari Takakura. Himari passes away after going out on a trip with her brothers. She was however, miraculously saved by a spirit thriving in a penguin-shaped hat. In return for her extended life, the twins must search for an item known as the Penguin Drum with the aid of three penguins which are visible only to the siblings.

Yukiteru Amano (Yuki) is a loner who never really interact with people and prefers writing a diary on his cell phone with his only companion being an imaginary friend named Deus Ex Machina, the God of Time and Space. However, Yuki soon learns that Deus is not a figment of his imagination but real when Deus makes him a participant in a battle royale with eleven others. Within this "Diary Game", the contestants are given special diaries that can predict the future with each diary having unique features that gives them both advantages and disadvantages.