Baxter Stockman is scolded by Shredder and Rahzar for his inability to create efficient mutant henchmen. As punishment, the Shredder finally activates his mutation collar, causing Baxter to turn into a mutant fly.
Elsewhere, Donatello has managed to create two samples of retromutagen, hoping to use one to restore Kirby Bat to his human form and one to restore Splinter to the form of Hamato Yoshi.
The Turtles end up in a new field of danger when one of their samples of retromutagen gets lost and both Rahzar and Baxter are fighting them to get the last sample and use it on themselves.
- Casting Gag: When Michelangelo wonders what he'd look like if he turned human, a picture of Greg Cipes, his voice actor, appears.
- Cerebus Syndrome: The context for Baxter's transformation, Shredder punishing Baxter for repeated failures, is showcased by having Shredder barely hesitate when detonating the Mutagen collar, and afterward, Baxter's plight at being a fly man has near-completely driven him insane, leaving most of his humorous traits behind.
- Chekhov's Gun: April is immune to mutagen, remember?
- Comically Missing the Point: When Donatello explains the properties of the retro-mutagen to his brothers and mentions his intentions to cure Kirby and Splinter, Michelangelo wonders how he'd look if the retro-mutagen was used to turn him human. Raphael has to spell it out for him that rather than turn Mikey human, it would just turn him into an ordinary turtle.
- Earn Your Happy Ending: Kirby O'Neil is finally restored to his human form and reunited with his daughter April.
- Foreshadowing: While attempting to defend his experiments, Baxter tells Shredder about the possibility of mutant pigs and rhinos. Bebop and Rocksteady make their debut a year later.
- Hope Spot: Baxter breathes a sigh of relief when it appears the collar failed to activate, but it turned out to be delayed.
- Mythology Gag:
- The "useless mutant" Shredder yells at Baxter for creating is shown in a photograph to be Ace Duck, a character who originated as an action figure in the 1987 cartoon's toyline.
- Baxter mutating into a fly is also a reference to the fate of his 1987 cartoon counterpart.
- When the retromutagen is first shown, Michelangelo expresses interest in using it to become human. The 1987 episode "The Gang's All Here" did involve Mikey temporarily becoming human.
- Baxter Stockman suggests to Shredder that he can create mutant pigs and rhinos, a reference to Bebop and Rocksteady.
- Naked on Revival: When Kirby turns back to normal, he asks why he's nude. Thankfully, we don't see anything since the turtles placed a tarp on him.
- Not Helping Your Case: Stockman tries to label Ace Duck a triple threat since it swims, flies, and knows Taekwondo, which obviously doesn't appease Shredder's anger.
- Not Quite Dead: Shredder allows Baxter to live on the condition that he creates more mutagen mutants.
- Sadistic Choice: After Donatello sees that he only has one sample of retromutagen left and knows that it would take months to make some more, he is conflicted over whether to use it on Kirby or on Splinter. Splinter insists that Kirby needs it more than he does. In the end, it is used on Kirby and Splinter informs his son that he is content with staying a mutant rat.
- Sanity Slippage: Baxter wasn't all there to begin with, but after mutating into a fly, he's gone completely off the deep end.
- "Shaggy Dog" Story: Narrowly subverted. At the end of the climactic fight scene, the last sample of retromutagen breaks, seemingly rendering everyone's attempts for it All for Nothing...but April manages to direct Kirby under the last drop, turning him human again.
- Stranger in a Familiar Land: Discussed. When Donatello apologizes for not being able to cure Splinter, the latter makes it a point that such a thing wouldn't change much. After 15 years as a mutant rat, Splinter concedes that human society would be alien to him at this point, and he's more content with the company of his turtle sons.
- Trademark Favorite Food: After mutating into a fly, Baxter seems to enjoy consuming candy bars.
- Whole-Plot Reference: Baxter planning to cure himself by redoing the mutation process with another human to dilute his fly DNA is nearly identical to what happens with Seth Brundle in The Fly. Stockman even paraphrases Seth's last words when outlining his desperate scheme.
- You Have Failed Me: Shredder finally has enough of Baxter's screw-ups and activates his collar.
