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.
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 second mutation. Another plan that was discussed was to add a fifth 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).
In the original comics, the Time Scepter is normally associated with Renet, the timestress apprentice of Lord Simultaneous. She often encounters Savanti Romero. None of these characters appear in this film.
The concept for this movie is loosely based on a story called "Masks" from issues #46 and #47 of the original Mirage comics. The story features the Turtles and Renet traveling back to Feudal Japan to fight an evil shogun and engage in samurai battles.
This is film is part of a multi-media Feudal Japan Ninja Turtles event with the "Masks" story first appearing in the Mirage comics in 1992, the third film released in early 1993, and the Turtles and Splinter traveling back to Feudal Japan to fight Shredder in a late 1993 episode of the Teenage Mutant Ninja Turtles (1987) cartoon. Since then, traveling back to Feudal Japan has been a staple for the Turtles.