Baxter Stockman's transformation in the original series was an homage to the classic horror film The Fly (1958). His transformation in this series is more similar to the transformation Jeff Goldblum goes through in the remake The Fly (1986). As in that film, Baxter slowly mutates rather than being instantly transformed. He also develops a habit of eating candy bars and keeps his body parts in jars. His final solution is to subject April to the mutagen, just as Brundle attempts to put Ronnie through the matter transporter.
When Michelangelo begins to wonder what he would look like as a human, his head briefly turns into a poorly-animated version of his voice actor Greg Cipes.
Stockman suggests mutating a pig and a rhinoceros. This is in reference to Bebop and Rocksteady, the first two mutants in the original animated series.
When shredder shows disappointment in stockman's latest mutant creation, he gives him a photograph of a mutant duck. The name on the bottom of the picture says Ace Duck which was a character in the original TMNT toy line that was noted as being able to do Taekwondo