The year is 1580. Using an army of soldiers equipped with sophisticated weaponry, Nobunaga Oda is on the verge of ruling Japan with an iron fist. One of his enforcers is Ginnai Doma - a fallen samurai reborn into an indestructible killing machine. As Ginnai continues his killing spree on ninjas and those who oppose Nobunaga's rule, Shishimaru of the Iga Ninja - going against the Koga Ninja's plans - pursues a one-man vendetta to avenge the deaths of his comrades and kill the immortal warrior.

Years ago, the opening of an interdimensional portal released two beasts into the skies over the Sea of Japan, visible to all the countries along the coast. After destroying the naval patrol sent to investigate the disturbance, the two beasts then turned against each other. Witnessing the fight from Japan, scientists Joe and Marie Hayakawa were sucked into the rift. Upon returning to Earth, they compiled and published the academic findings from their voyage in a legendary book titled ''Day of Succession''. Attempting a second expedition to that other dimension twelve years later, the couple have not returned. Twins Ai and Yu Hayakawa decide to set forth in search of their parents and the mysterious Wonderland they studied. In the ruins of an abandoned subway station, the two wait for a train to take them to the world beyond. On board they meet Lisa Pacifist, who quickly decides to aid the two in the search for their missing family. Can the three of them manage to find Joe and Marie?