The TMNT, Ninjara and Splinter are relaxing in the lair when an intruder arrives - a fox dude that turns out to be Ninjara's brother, Naga. The young fox states that he has come because Ninjara's grandmother has been captured by a hunter. Raph demands to know how the mutant found their secret lair, and Naga states that Ninjara gave him directions. This upsets Master Splinter and the TMNT, and Ninjara apologizes, saying that she only told her brother where she was. Raph isn't appeased by her apology, but before an argument can erupt, April suddenly appears on the TV giving a report about a giant, four armed creature attacking the city. The Turtles announce that they've got to investigate, but Ninjara states that she has to leave with her brother. Raph asks Splinter if he can accompany her, and the Sensei grants him permission and tells his student that he must release his anger concerning Ninjara giving away the address to their lair.
Of course, Raph doesn't do this. The three stow aboard a plane to Japan, and Raph badgers Ninjara about telling her borther the secret. Ninjara screams at him to shut up and the two fall into angry silence, leaving Naga to awkwardly try to make peace for the duration of the long, long flight. Once the trio lands, they take a boat to an island hidden by clouds, the home of Naga and Ninjara. The children welcome the foxy ninja home, but an Elder is not happy to see her because she has left her people. Kenji, Ninjara's old boyfriend, tells our heroes that the Council of Elders has decreed that no rescue will be attempted for Ninjara's grandmother.
The next morning, Raph, Ninjara and Naga set out on their own to rescue the foxes' grandmother. No sooner have they entered the forest when Ninjara and Raphael are ensnared by a trap net. Ninjara orders Naga to cut them free, but the youth reveals that he's made a deal with the hunter - he's offered the man Raphael in trade for his grandmother. The hunter arrives and decides that he will keep both Raph and Ninjara as his trophies. Naga tries to argue, but the hunter smashes him in the head with the butt of his rifle and then shots the netted Raphael with a tranquilizer.
Raph awakes in a cage next to Ninjara in the hunter's trophy room. Naga and his Grandmother are there as well, though they are not caged. The man gloats, which sends the Elder fox into a rage and she attacks. Naga uses the distraction to open the cages, and Raphael punches him in the face for betraying them. Ninjara notes that they can settle their dispute with her brother later, right now they need to escape. A fire bursts into life and the mutants head outside, where they find themselves stranded upon a high cliff. Grandmother explains that they'll have to escape via the Underworld - a place Raph is not interested in visiting, but a huge explosion rips out of the hunter's building as his ammunition begins to ignite. The blast convinces the Turtle that they'll have to go through the Torri gate to make their escape. Just then the hunter arrives and begins firing his pistol at our heroes. Raph is able to hold him off while the Elder fox opens the gateway to the Underworld. The four mutants jump through the portal, but the hunter chases them and manages to get through the gateway before it closes.
The five outworlders arrive in the Underworld and are welcomed by a demon, who tells them that they can leave via the Torri that they arrived in. The hunter makes a dash for the gate, but rather than passing though a portal to his dimension, he simply plunges through the framework and falls into the pit. The demon asks if she had forgotten to mention that it only works for the pure of heart. Grandmother decides to test if the demon is telling the truth, and walks through the Torri, vanishing. Naga is next, and he too disappears. Ninjara and Raph embrace, and then run to the Torri holding hands.
The couple pass thorugh the Torri and arrive on Ninjara's home island, where they are greeted by Grandmother and Naga. Ninjara compliments her kin on her fighting ability and Raphael makes peace with Naga.