In Japan, the year 1603, a lone warrior on horseback races through the forest, being chased by four Samurai. The young man is captured by his pursuers and taken to the imposing Fortress of Lord Norinaga. Inside, Lord Norinaga confronts his captive, his son, Prince Kenshin. Norinaga quarrels with Kenshin, who is ashamed of his father's actions in what he considers to be an unjust war. Just as Norinaga is about to strike his son down for disgracing him, a gunshot is fired. An English trader, Walker, warns Norinaga that the rebels are about to attack. Guards take Kenshin away as Norinaga and his British allies prepare for battle.
In present-day New York City, the Turtles are in their sewer abode, practicing their ninjitsu skills. April appears to present gifts to the Turtles as they have offered to watch her apartment while she goes on vacation. She brings an odd scepter along to give to Master Splinter which begins to glow magically. In a flash, April disappears, and in her place is an Asian man: Prince Kenshin.
April finds herself back in time at Lord Norinaga's fortress. Everyone there, save for Walker, thinks that she is a witch, and April tries to use this to her advantage by frightening the ancient warriors. Walker, disbelieving that April has any supernatural powers, defies her to shrink him. When she fails to perform the sorcery, guards haul her away.
Back in New York, Donatello and Splinter have determined that the scepter is a time-switch device, and for the Turtles to use it, people from the past will be brought to the present. The Turtles get their friend Casey Jones to guard the people from the past that will appear when they go back in time to find April. Donatello determines that the staff's powers will only work for 60 hours, and after that time, if the Turtles do not return, they will be stuck in the past. Don activates the Scepter, and in a blinding flash, the Turtles vanish. In their place are four disoriented Samurai, the four Honor Guards of Lord Norinaga.
The Turtles pop back in time into the middle of the battle between Norinaga's forces and the rebels. They are on horseback and decked out in full Honor Guard Samurai regalia. Michaelangelo ends up backwards on his horse, and it gallops out of control into the forest! He is attacked and dismounted. The leader of the rebellion, Mitsu, is shocked to find a giant Turtle under the helmet, and she orders Mikey to be carted off to the rebel village. As night falls, the 3 remaining Turtles sneak into Norinaga's keep in attempt to rescue April. Walker is talking with Norinaga, who has just learned that his four Honor Guards have disappeared, along with the Sacred Scepter! Walker argues that Norinaga must buy his guns to quell the rebellion, while Norinaga fears that all is lost now that the scepter has vanished.
The Turtles follow Walker's henchman, Niles, and he inadvertently leads the Turtles to April in Norinaga's dungeon. April finds an escape route, and she and the Turtles fight their way to escape. They are accompanied by a prisoner named Whit, who bears an uncanny resemblance to Casey Jones. It seems that he was jailed for mutiny, and he is as eager to leave this place as April and the Turtles are.
Norinaga, when discovering April's escape, prepares to punish Niles. Walker is able to prevent his henchmen from being toasted, however. The Turtles are now in the forest, basking in its ancient beauty. Suddenly, rebel forces ambush them, thinking that they are Norinaga's Honor Guard. Donatello removes his helmet, and the rebels are shocked to see more giant Turtles. The Turtles are taken to meet Mitsu, who exclaims that they are like "the other one." The Turtles realize that Mikey is with the rebels and rejoice in the knowledge that they'll soon be reunited. As they head back to the rebel village, they see smoke rising from it. Walker and his men are burning the town, looking for the scepter and Prince Kenshin. As the Turtles and the rebel warriors rush to save the town, we see a young boy trapped in a burning home. Mikey rescues the child and Leo saves his life by performing CPR. Mitsu now knows that the Turtles are good, and welcomes them. The Turtles remember that they need the scepter to get back home, and they are running out of time. They go in search for it, as Whit and April help the townspeople rebuild their homes. When the Turtles cannot find the scepter, Donatello comes up with the unlikely scheme of creating a new one. When Donatello's scepter is finished, Leonardo accidentally drops and breaks it. Just then, Mitsu walks in and announces that Norinaga will attack in the morning. The Turtles decide to join Mitsu and her people to fight the overlord.
That night, Michaelangelo and Yoshi hang out. Raphael gives Yoshi a yo-yo, and the boy wanders off. When he returns, he brings the Sacred Scepter. As everyone argues about who hid the scepter, Whit holds a knife to Mitsu's throat and demands the scepter. Whit takes Mitsu to Norinaga, and tells the Daimyo that she has kidnapped his son Prince Kenshin. Mitsu then tells Lord Norinaga that Whit is holding the Sacred Scepter. Mitsu attacks Norinaga but is stopped by Walker, and she is taken to the dungeon. Whit tries to cut a deal with Walker, using the Sacred Scepter as a bargaining chip.
The Turtles break into the castle once again to save Mitsu and the other rebel captives. As the heroes attempt their escape, they run headlong into Lord Norinaga and his men, and a battle ensues. Leonardo manages to beat Norinaga in a sword fight, and effectively captures him inside a giant bell. Things are going great for the Turtles when Walker takes April hostage at gun point. Walker tries to flee with the Sacred Scepter, but the Turtles catch up with him. Walker tosses the staff into the air, but the Turtles manage to catch it before it hits the ground and breaks. A fireball explodes then, knocking Walker off the top of the castle and into the moat waiting far below. Back in New York, Casey realizes that it is time to send the real Honor Guard back to the past, but they have lost themselves in a local nightclub.
The Turtles have the Sacred Scepter at last and the rebels have defeated the evil overlord Norinaga. As the Turtles prepare to use the Scepter, Mikey, Raph and Leo decide that they would like to stay in the past, where they are welcome and happy. As they argue, the magic staff activates, and the Turtles make the decision to leave. Now back in the sewer, the four Honor Guard and Prince Kenshin have vanished, and in their place are April and the Turtles. Casey and Splinter welcome the Turtles and April home.
