JAPAN, 1603: A lone warrior races through the forest, being chased by four Samurai on horseback. The young man is captured by his pursuers, and taken to the imposing Fortress of Lord Norinaga. Inside, we see Lord Norinaga confront his captive, who we find to be his son, Prince Kenshin. Norinaga quarrels with his son, 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, we hear a gun shot fired. Enter Walker, a conniving English trader. He warns Norinaga that the rebels are about to attack. Guards take Prince Kenshin away, as Norinaga and his British allies prepare for battle.
NEW YORK CITY, The Present: We find the Turtles in their sewer abode, practicing their ninja skills. April appears to present gifts to the teen terrapins as they’ve offered to watch her apartment while she goes on vacation. She’s brought an odd scepter along to give to Master Splinter… which begins to glow with weird magic. In a flash, April disappears, and in her place is a 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 the TMNT 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 don’t come back, they’ll be stuck in the past! Don activates the scepter, and in a blinding flash, the Turtles are gone! In their place we see four very confused 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’re 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 TMNT 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 looks amazingly like 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 TMNT 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’re running out of time! They go in search for it, as Whit and April help the townspeople rebuild their homes. When the Turtles can’t find the scepter, Donatello comes up with the unlikely scheme of creating a new one! April is very skeptical!
Meanwhile in the present, Casey Jones keeps the four Honor Guard busy by teaching them to play hockey!
Back in the past, Michaelangelo introduces the villagers to pizza, and Whit tries to convince April to take him back to New York City. Donatello’s scepter is finished, but Leonardo drops it and it breaks! It seems as if the TMNT are trapped in the past! 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, Raph 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. Michaelangelo is injured accidentally by Mitsu! Leonardo manages to beat Norinaga in a sword fight, and captures him in a giant bell! Things are going great for the Turtles when Walker takes April hostage at gun point. Leo challenges the vile Brit, and Walker fires a cannon at the bold Turtle… but misses Leo and hits the bell that imprisons Norinaga! Walker tries to flee with the Sacred Scepter, but the Turtles catch up with him. Walker tosses the staff into the air, but the TMNT manage to catch it before it hits the ground and breaks! A fireball explodes from nowhere, knocking Walker off the top of the castle and into the moat waiting far below.
Back in New York, Casey realizes that it’s time to send the real Honor Guard back to the past… but he’s taken them out to a nightclub! They hurry back to the sewer.
The Turtles finally have the Sacred Scepter and the rebels have finally defeated the evil overlord Norinaga. As the TMNT prepare to use the scepter, Mikey, Raph and Leo decide that they’d like to stay in the past, where they are welcome and happy. Don says no way! As they argue, the magic staff activates! With a flash, the TMNT and April are gone!
Back in the sewer, the four Honor Guard and Prince Kenshin have vanished, and in their place we see April and the Turtle team. Casey and Splinter welcome the Turtles and April home. Michaelangelo laments for a moment, but quickly realizes that home is where the heart is… even if home is a sewer!