Japan gave up its independence in order to avoid total collapse after the outbreak of an alien virus. 10 years later Japan is still a dependent nation under a not-so-friendly provisional government called GHQ. At the same time, a boy named Shu has lost his past memories and himself. By chance Shu comes in contact with the beautiful and stoic Yuzuriha Inori and the resourceful and charismatic Tsutsugami Gai, both members of a militant resistance group called the Undertakers. Through his interaction with the members of the Undertakers and his acquisition of a genetically based power, the conflicted and withdrawn Shu slowly learns how to connect with others and reclaim himself. When GHQ falls into the hands of a man who intends to use the virus to 'reset' earth's population, Shu and the Undertakers fight to stop him and reclaim Japan.