In the present, Mr. Takagawa, the curator of a museum of ancient history in Tokyo, and Kenji, a janitor, witness an exhibit of the Black Samurai seemingly come to life.

The next day, the Mystery Inc. gang travel to the prestigious Mirimoto Academy near Tokyo for a martial arts tournament that Daphne Blake was invited to participate in.

Though the warrior leads an army of ninjas in attacking the academy and seemingly steal the scroll, Mirimoto reveals he stole a copy and presents the real one to the gang.

After Shaggy Rogers and his dog Scooby-Doo unknowingly solve the riddle, Mirimoto sends the gang to find the Sword of Doom before the Black Samurai.

Moreover, Miyumi betrays the gang to side with Mirimoto, who subsequently captures most of Mystery Inc. and Takagawa, but Daphne passes the Sword of Doom to Shaggy and Scooby, who escape on a jetpack.

Though they are pursued by the robots, who steal the Sword of Doom, the pair are rescued by Matsuhiro, a sushi shop owner and samurai who agrees to train them in his ways.