Raphael recovers the missing time scepter from Yoshi who hid it in the basement of his house and gave it to Raphael so he and the other Turtles wouldn't have to fight Lord Norinaga and Walker's forces the next day. After showing the other Turtles and April (Paige Turco) the scepter, the Turtles soon come to believe that Mitsu (Vivian Wu) was responsible for hiding it, so the Turtles would have to stay and fight Norinaga and Walker. Yoshi's grandfather comes and reveals that he was the one who hid it, so they would fight the battle and not Mitsu. Whit shows up, holds Mitsu hostage, and the Turtles hand the scepter over to him so he wouldn't hurt her. He tells them to bring Kenshin to Castle Norinaga that night, and he'll free Mitsu, and he tells them that they'd better be gone by morning after that. April decides to go ahead of the Turtles to try and negotiate with Walker and Whit, but she is captured upon arrival at Castle Norinaga.
The Turtles emerge from the castle dungeon's sewer, free Mitsu and the other prisoners, and they and the village rebellion lay siege to the castle. Leonardo defeats Lord Norinaga in a swordfight, and traps him in the castle's bell. Then, Walker and his gun-toting crew shows up, and Walker orders them to shoot them. Whit protests, saying that that wasn't part of their deal, and Whit is placed in the line of fire with them. Leonardo soon coaxes Walker into having him shoot them, but when Walker fires up his cannon, Leonardo retracts his head into his shell, and the cannonball collides with the top half of the bell and smashes it. The Turtles and the villagers then ward off Walker's forces while Walker escapes. He grabs the scepter and his finches and heads for the roof, with the Turtles soon in pursuit.
Walker is cornered at the castle's edge, and he throws the scepter into the air to distract the Turtles as he makes his getaway down the castle's exterior wall. As he reaches for his finches, Whit fires a catapult at Walker, sending a napalm burst at him, which knocks Walker off the edge into the raging ocean below. As the Turtles wait for midnight to strike to take them home, Michaelangelo and Raphael decide to stay, the former because of Mitsu. Mitsu and Yoshi show up to wish them off, but when they learn of what Mikey and Raph plan to do, Mitsu (and the others) talks them out of it. When the scepter takes them back home to present day New York, Michaelangelo is almost left behind in feudal Japan, but some remaining power in the scepter manages to make it take him back home just moments before midnight. Back in feudal Japan, Kenshin reconciles with his father Norinaga and kisses Mitsu, and in the present Michaelangelo gets cheered up and dances with the other Turtles.
Thanks Tornado Dragon!