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A young woman, by some strange occurrence, was left to die alone in the former building of the Academy for Sincere Teachings. Mysteriously, there is one person who can see her in ghost form: Niiya Teiichi, a freshman.

Yukiteru Amano (or 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.

Yukiteru Amano kept a diary he wrote in each day. He was always the bystander.

Set in a slightly futuristic world, Earth has been invaded and is at war with aliens from another dimension called the Nova. In order to counter them, Pandoras and Limiters, genetically modified girls with super fighting skills and their male partners who use special "freezing" powers to limit their opponent's mobility, are made to fight against the Nova.