After the human colony on the moon was destroyed by disease, Kyousuke Date and his mother flee to Earth—separated from their family. They take refuge in a cathedral where his mother hides as a nun for reasons unknown to Kyousuke. After dangerous people find their sanctuary, his mother stabs him before she herself is murdered.

Days later, Kyousuke finds himself alive and in the house of a mysterious girl who claims to be his twin Runa—and she is not the only one! Runa suffered a similar fate at the hands of her adoptive mother; however her soul was divided into several pieces making "flicker girls" who are being hunted by the evil Kirihara Group. The reason Kyousuke survived: his body's DNA conformed to the disease and he is able to transform into a fearsome alien mutant known as the SoulTaker.

Kyousuke begins his battle against a hospital of evil mutants and dangerous corporate assassins in order to save himself and the sister he has never known.