Some TMNT stuff really isn't for little kids.
The TMNT are teleported to a world of talking animals—the world of Usagi Yojimbo! When the samurai rabbit embarks on a quest to save Japan and the deadly Jei blocks his path, a Turtle team-up may be the only chance for survival!
Usagi singlehandedly defeats a number of bandits, eventually scaring them off with his sheer skill and ferocity. A nearby group of pilgrims thanks him for saving them, and reveals that "the old one" assured them that Usagi would protect them from the bandits. Usagi has no idea who they're talking about, but is told to go to "the cave in the green grotto" where the mysterious person is waiting for him.
On his way to the grotto, an earthquake strikes, which Usagi reflects is happening more often lately. He discovers that the person waiting for him is Kakera, who informs him that he needs Usagi's help to take a valuable object to Tashima Shrine. Unfortunately there is someone who wants to stop him, which is why he needs help - not just from Usagi, but from some traveling companions that Usagi already knows.
Usagi heads out to the grotto and finds four small turtles, and Kakera recites a spell that transforms the four ordinary turtles into the mutant ninja variety. The Turtles are very disoriented by what has happened, especially since they can't understand anything that Kakera and Usagi are saying. Raphael attacks Kakera but is easily defeated.
Michelangelo, Raphael and Donatello charge again at Kakera, while Leonardo attacks Usagi. Usagi is confused by this, since he and Leonardo are friends, and suspects that his friend has been possessed by a demon. Leonardo, meanwhile, has no idea who Usagi is and suspects he's some kind of mutant enemy. The two are evenly matched, but their fight is interrupted by Kakera, who causes them all to suddenly understand each other's languages. He reveals that these are not the Turtles that Usagi is familiar with, but Turtles from a different reality.
On the way to the shrine, Kakera shows the Turtles and Usagi the valuable object - a piece of rock. He explains that a giant catfish named Namazu lives under their land, and its slightest movement can cause earthquakes. It was pinned in place by the thunder god Kashima-no-Okami, using a massive rock called Kanameishi, but he later broke off a piece of the rock during an argument with the other gods. As a result, the Kanameishi's power has diminished and Namazu is gaining strength. If they don't complete their quest, the entire land will be destroyed.
Kakera also tells them that someone is trying to stop him: Jei, an evil sorcerer who believes himself a servant of the gods. Jei is following them at a distance with a large number of bandits, whom he believes are enough to defeat Usagi and the Turtles. He believes that the gods have sent him to destroy evil, and there won't be any more evil if the entire land is destroyed. One of the bandits tries to leave, and is brutally killed by Jei.
Kakera, Usagi and the Turtles arrive at Kashima Shrine, but are immediately attacked by Jei's followers. Though they are outnumbered, they are able to hold their own against the bandits, but Leonardo and Usagi find Jei to be a more difficult opponent, both being defeated by him. Meanwhile, Kakera makes his way to Kanameishi and begins the spell to reunite the stone fragment with the larger rock, which leaves him vulnerable to an attack by Jei. But before Jei can stab him, Kakera finishes the spell and a massive explosion erupts from the Kanameishi.
When Usagi and the Turtles wake, all the remaining bandits have fled, and the Kanameishi has buried itself more securely in the Earth. Leonardo is interested in staying in Usagi's land for awhile and exploring, but Kakera says that is for another time.
The Turtles and Usagi say their goodbyes, with Leonardo and Usagi expressing a desire to meet again and test their skills against each other. Kakera returns the Turtles to their own reality, leaving only four ordinary turtles behind. Usagi returns the turtles to a pond, and bids farewell to Kakera, but Kakera hints that they will meet again, when Kakera needs him again.