In 1603, during Japan's feudal era, a young man finds himself on the run, pursued by four samurai on horseback. As they enter the thick woods, a mysterious woman observes from the shadows. Unfortunately, the samurai soon capture the young prince, known as Kenshin.
Fast forward to the present, two years after the defeat of The Shredder and The Foot Clan, April O'Neil is preparing for her upcoming vacation at a flea market. In a gesture of kindness, she gathers gifts for her friends, the Teenage Mutant Ninja Turtles, at their underground lair. Among the treasures, Michelangelo receives an antique lamp—wearing the lampshade as a hilarious Elvis Presley homage, Donatello is tasked with fixing a broken radio, Leonardo gets a book about swords, and Raphael is supposed to have a fedora, but due to his earlier outburst, he is left empty-handed. She also presents Splinter with an ancient Japanese scepter.
In a moment of familial tension, Kenshin faces his father, Lord Norinaga, who reprimands him for tarnishing their family’s honor. Kenshin, however, argues that his father's thirst for war is the real disgrace. Their heated discussion is interrupted by Walker, an English trader bringing additional men and firearms to support Norinaga. Kenshin departs to the solitude of a temple, where he discovers the very scepter brought to the present by April, inscribed with the words: > "Open Wide the Gates of Time".
Back in modern times, April examines the scepter, which suddenly begins to glow, enveloping her in a whirlwind of mystique. She is unexpectedly transported back in time, while Kenshin is swapped into her place, with each donning the attire of the other. In this strange new world, April faces accusations of witchcraft, but Walker quickly realizes she possesses no powers and has her imprisoned instead. Meanwhile, Kenshin, bewildered by the presence of the turtles, misidentifies them as "kappa". Upon learning about April's plight, the turtles vow to embark on a rescue mission, but they must act within sixty hours; otherwise, the scepter's powers will fade away, disrupting the space-time continuum. To safeguard Kenshin and the lair, they enlist Casey Jones and utilize the scepter to leap through time, but the process causes Norinaga's Honor Guards to take the turtles' place.
Once in the past, the turtles awaken in a chaotic scene, attempting to manage their new mounts. Amidst the confusion, Mikey inadvertently separates from the group, leading to a surprise ambush from a mysterious attacker. Meanwhile, the rest infiltrate Norinaga’s castle, using their disguise as Honor Guards to search for April. Unfortunate circumstances unfold when they rescue not only her but also another prisoner, Whit, who has been imprisoned for opposing Walker’s regime; however, they find themselves stranded in the wilderness without a clear plan. Back in the present, Kenshin grows restless, expecting a confrontation with Casey, who, instead, introduces him and the Honor Guards to the sport of hockey, bringing temporary amusement amidst anxiety.
In the woods, the turtles, April, and Whit encounter hostility from villagers who mistake them for soldiers of Norinaga. This conflict ceases when Mitsu, leader of the rebellion, recognizes Raphael as the spitting image of one of her captured warriors. The turtles soon realize she is seeking Mikey, and they accompany her back to her village, which is currently under attack from Walker's men. As they join forces with the villagers to fend off the assault, Mikey is liberated by some bumbling guards and rushes to their aid. Walker is compelled to retreat, but a young boy named Yoshi finds himself trapped in a blazing house. In a heroic act, Michelangelo saves Yoshi and is later revived by Leonardo's CPR, earning deep gratitude from the villagers.
With negotiations ongoing between Walker and Lord Norinaga regarding weapon sales, the turtles settle into village life. Donatello takes the initiative to craft a replica of the scepter for their return journey, while Mikey shares the joy of pizza with the villagers and comforts Mitsu about her feelings for Kenshin. Meanwhile, Raphael forms a bond with Yoshi, teaching him emotional control. Back home, the Honor Guards adapt to contemporary life, leading Casey to challenge them to a hockey match, which devolves into chaos as they misinterpret the game’s rules.
In the past, the replica scepter is completed, but a spat between Michelangelo and Raphael results in its shattering, complicating their situation further. Mitsu reveals that Norinaga plans to attack her village at dawn, sparking urgency among the turtles. When Raphael sneaks off to see Yoshi, he discovers the original scepter in the child’s possession. This revelation brings joy but also frustration, as the turtles learn Mitsu had concealed it to compel them into her battle. Intriguingly, Mitsu's grandfather reveals that this plan was his suggestion.
Suddenly, betrayal strikes from Whit, who captures Mitsu and seizes the scepter before fleeing. The turtles spring into action, storming Norinaga’s palace to rescue her. After a gripping showdown with Norinaga’s soldiers, the turtles free the imprisoned warriors, igniting a massive battle in the palace grounds. In a climactic duel, Leo bests Lord Norinaga, humorously finishing him off by trimming his hair and trapping him in a bell. As Walker attempts a getaway with the scepter, he is cornered, and in a desperate move, he throws it to distract the turtles. They catch it, and with a change of heart, Whit aids their cause by launching a fireball at Walker, leading to his demise.
With preparations underway to return home, Mikey hesitates about leaving Mitsu behind, and Raphael contemplates staying in a land that cherishes their contributions. The rest of the turtles and April insist on returning, while Kenshin activates the scepter, intensifying the dilemma. Following an emotional discussion, Mikey reluctantly decides to go back with his brothers. In a last-minute twist, the Honor Guards swap back with the turtles—except for Mikey, who narrowly misses rejoining them. Thankfully, the loyal Honor Guard Benkei activates the scepter again just before it fails, switching places with Mikey.
In the past, Norinaga ultimately concedes to Mitsu and Kenshin, presenting the scepter back to them. As the two lovers rejoice in their reunion, back in the present, Michelangelo grapples with the reality of growing up. Yet Splinter uplifts his spirits by mimicking Mikey's earlier Elvis impression, prompting the turtles to join in a lively final dance celebration.
