In ancient Japan, a rebel leader named Kenshin accidentally exchanges places with April O'Neil, a friend of the titular anthropomorphic turtles, through the power of a mystical scepter. April, who finds herself in the past, is taken by the shock, while Kenshin lands in modern-day New York, where the Ninja Turtles and their master Splinter reside. Unnerved by the temporal swap, the turtles decide they must travel back in time to retrieve April. Donning the garb of samurai, they use the scepter to make the time jump, but the transition brings unexpected complications.

Upon their arrival in the past, the turtles find themselves embroiled in a conflict between a group of oppressed villagers and a warlord who is allied with an unscrupulous British trader. The turtles, realizing they're caught in a battle for freedom, must navigate the challenges of this foreign land while seeking to rescue April. Meanwhile, the scepter that serves as their ticket home is in jeopardy, creating tension as they grapple with the need to support their new allies in their fight against tyranny, and the urgency to return to their own time before it becomes impossible.