Kei Nagai dies in a car accident, but realises he is a type of immortal known as Ajin. Hunted by humans, Ajin is eventually found by the government and used as a subject in cruel experiments. He finds fellow demi-humans along the way as he escapes and goes on the run.

In 1868, after the Bakumatsu war ends, the ex-assassin Kenshin Himura traverses Japan with an inverted sword, to defend the needy without killing.