The story is told from a third-person perspective by the Ninja Clue Book.Clumsy Ninja is the next generation of interactive characters!

He has a unique sense, perception, action and reaction every time. Prepare to be amazed! ...... Oh, and please take care of him! The main objective of the game is to save Kira, the clumsy ninja's training partner and friend, from her rival Hori-Bull, whose main objective is to find the Dragon Medal. Kira finds the Dragon Medal before Hori does, but loses it because Hori-Bull weakens her, as described in the storyline. Clumsy Ninja, Lily, Chick, Squirrel, and Sensei come to the temple setting/area to find Kira and rescue her from Hori-Bull (Hori-Bull stuffs a jelly potion into Kira's stew that disables her limbs. Then throws her sword into the river, locks it in the car, gets the dragon's badge, and takes Kira to the temple area, where Kira manages to write a warning in her diary and give it to her dum-dums, who also find Kira's sword.

They currently open the dojo, only to find Kira and Holly Bull as stone statues. After releasing the duo, a battle also ensues.