Set many years after the end of the original Ultraman Tiga series, in which Daigo Madoka (human host of Ultraman Tiga) has a son with Rena, named Tsubasa Madoka. Tsubasa is a member of a new team, Neo Super GUTS, the successor to the original Super GUTS.

Nathan Algren is an American hired to instruct the Japanese army in the ways of modern warfare, which finds him learning to respect the samurai and the honorable principles that rule them. Pressed to destroy the samurai's way of life in the name of modernization and open trade, Algren decides to become an ultimate warrior himself and to fight for their right to exist.

A group of female commandos confront evil criminals Zombie-Man and Zombie-Woman.