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Shibusen, standing for Death Weapon Meister Academy (DWMA) the technical school for Reaper Armsmasters that operates from the deepest recesses of all the corners of the world, in order to prevent the second coming of the so-called Demon God who is feared upon bringing destruction of all humankind and envelop the world with nothing but madness and darkness. The reaper built this agency for weapons and for those who will be trained to wield them.

Yukiteru "Yuki" Amano is a loner who spends most of his time writing a diary on his cell phone or talking with his imaginary friends Deus Ex Machina, the God of Time and Space; and Murmur, Deus' servant. One day, Deus gives Yuki a special diary, mentioning something about a game.

Mutated homo sapiens that have a dangerous telekinetic power is being captured and isolated in laboratories by the government. One of the sixth-sense-possessing humanoids escapes loses her memories and winds up living with a boy from her past.