Turtles Forever

In the original Teenage Mutant Ninja Turtles (1987) series from the 1980s, the Turtles often broke the fourth wall, and talked directly to the audience. This wasn't the case however with the Teenage Mutant Ninja Turtles (2003) series. This is made reference to in this movie, as the 1980s Turtles break the fourth wall several times. Until finally, Hun gets fed up and begins to violently shake the 1980s Raphael, while asking, "Why do you keep doing that?! Who are you talking to?! There's no one there!"

When the turtles first arrive in the 1987 dimension, all the background characters were taken directly from the Teenage Mutant Ninja Turtles (1987) cartoon's first episode, Teenage Mutant Ninja Turtles: Turtle Tracks (1987). Among them including Bebop and Rocksteady before they were turned into mutants and April's friend Irma. Several stores and buildings from the series, such as Channel 6, Ninja Pizza and Ninja Dentist, are also visible.

Due to 4Kids Entertainment being a non-union corporation, none of the voice actors from the Teenage Mutant Ninja Turtles (1987) cartoon show were able to reprise their roles in the film.

Mirage Leonardo's dialogue and inner monologue features several lines borrowed directly from the very first issue of Eastman and Laird's 1984 Teenage Mutant Ninja Turtles comic: "I cut two on the way down. Donatello takes out a third with his staff.""Shredder, we are here, Shredder face us! Shredder do you fear us?""The Shredder...has been shredded.""We are the Teenage Mutant Ninja Turtles. We strike hard and fade away into the night."

Among the mutated Foot Ninja, two members pass a resemblance to Tokka and Rahzar from the second live-action movie, Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991).