In the near future, a weary Logan cares for an ailing Professor X in a hideout on the Mexican border. But Logan's attempts to hide from the world and his legacy are upended when a young mutant arrives, pursued by dark forces.

Shishio sets sail in his ironclad ship to bring down the government. In order to stop him, Kenshin trains with his old master to learn his final technique.

Troubled by unsettling visions, young David Haller begins piecing together his fragmented memories and realizes he may have special powers.