The producion company decided to take the series in different direction after rising production costs and diminishing returns with each film. "TMNT: The Next Mutation" was a concept for fourth live-action. In this concept the Ooze that transformed the Turtles and Splinter was still in their bodies causing a much more drastic 2nd mutation. Another plan that was discussed was to add a 5th turtle named Kirby (named after comic artist Jack Kirby). However, the project got stuck in development and plans for a fourth theatrical live action movie was nixed. The concept of having the Turtles mutate into creatures was did see the light of day in the 'New Mutation' saga of the Teenage Mutant Ninja Turtles (1987) cartoon. Later the "Next Mutation" name and the idea of a fifth turtle, a female turtle named Venus Di Milo, was used in Saban's live-action series, Saban's Ninja Turtles: The Next Mutation (1997).
Starting in this film, All Effects Company took over and worked on the animatronic effects for the turtles and Splinter costumes. Jim Henson's Creature Shop was the company who worked on the mutant creatures in the previous two movies.
In the Teenage Mutant Ninja Turtles franchise, "turtles in time" is the theme for the 1st Super Nintendo game, the 2nd arcade game, the 3rd movie and the 4th game made for Nintendo (the previous three were for the original Nintendo Entertainment System).
In the original comics, the Time Scepter is normally associated with and used by Lord Simultaneous and his timestress apprentice Renet. They often encounter Savanti Romero. None of these characters appear in this film.
The concept for this movie is loosely based on issue #8 of the original Mirage comics which features one-off episodic style of storytelling. However, instead of traveling back to the 1400s Medival Earth, the Turtles travel back to Feudal Japan which actually better showcases their Bushido code.