Superfly’s plan of forced, unnatural selection isn’t just highly similar to the goal of Magneto in 2000’s “X-Men,” but reminiscent of “X-Men” comics in general, revealing TMNT’s general subtextual debt to Marvel’s own mutants. Ironically, the turtles are big Marvel Cinematic Universe fans (the MCU having not quite yet introduced mutants into their films), and it’s partially because of their innate sense of empathy and justice that they decide to try and stop Superfly despite empathizing with his and their fellow mutants’ wishes.
Sadly, the turtles not only fail in their attempt to stop the other mutants, but they also end up getting captured by Cynthia Utrom and her TCRI squad. One of the film’s great running gags is Splinter being adamant that humans will want to capture the turtles and milk them, a claim that the turtles regularly roll their eyes at. To their dismay, it turns out Splinter was more right than he knew, as Utrom hooks the turtles up to a milking machine (literally, that’s what it’s called) in order to obtain their mutagen-riddled blood for the purposes of manufacturing a mutant army.
Fortunately, Master Splinter gets tipped off by April as to the turtles’ plight, and the ninja rat saves his sons from any further malicious milking. It’s here that some of the revisions “Mutant Mayhem” makes to the Turtles’ legacy fall into place. Just like Eastman and Laird blended popular comics of their day into a heady stew, “Mutant Mayhem” director Jeff Rowe allows the film’s copious pop culture references to be a story point in addition to setting character and tone, going so far as to mix live-action source footage with the film’s animation. Here, Splinter isn’t a former human martial arts master, but a former rat who learned to perform and teach martial arts through kung-fu action movies. Thus, Splinter, the turtles, and the other mutants demonstrate a deep adoration of human culture, making it easier for them to accept that humans, despite their potential prejudices, aren’t necessarily the enemy.