Our story begins in the capital, where Shiren the Wanderer and his sidekick Koppa encounter an old friend. Known as "Sensei" he is both Shiren's uncle and his master, having taught him the way of the blade. Sensei offers Shiren a key that is said to unlock the legendary Karakuri Mansion, a labyrinth of dangerous traps, fell beasts, and treasure untold.

Shiren excepts the key, the wanderlust inside him striking his heart like lightning as he holds it in his hand. But this is only the calm before the storm...

The game's plot happens one year after Shiren the Wanderer GB2: Magic Castle of the Desert. Shiren and his partner Koppa reunites with his swordsman, Sensei, then led by him to embark on a journey to solve the mystery of the legendary Karakuri Mansion.