Immediately following the events of "Ikki tousen: Xtreme Xecutor", the kids from Nanyo Academy head to Kyoto for a school trip. Before long, they run into rival classmates from other Kanto schools and find themselves confronted by Kyoto's best fighters. It's a battle of epic proportions. Hopefully the city of Kyoto will be left standing!

An asteroid collision brought with it a deadly menace known as "Shinobi." Faced with destruction, humanity retreated to land reclaimed from the sea. The one ray of hope is a device that can fight the Shinbo called "The Mechanical Divine General." Ame, the princess of the refugees, and Suō, who carries the blood of the Yagyū family, must awaken its power in order to save the world.