An accident during tests of an anti-plasma artificial magnetic shield at Japan's Ground Self Defense Force East Fuji practice range sends the 3rd Special Experimental Company, under Colonel Matoba on a time-slip 460 years into the past, into 'the Age of civil War'. At the same time an imaginary-number anomaly thought to be caused by interference from the past begins eroding the present.

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.