In the series, Mikey did not come up with the nickname of "Buzzkill" for Baxter Stockman's fly mutant form, instead settling for mispronouncing his name.
Here Mondo Gecko is made human again, something that never happens in the original series.
Genius Ditz: Right after Miwa vents her frustrations about Mikey's mutation onto Baxter Stockman, Mikey instantly knows of her Guilt Complex. This leads to Miwa openly questioning if the mutation made him psychic.
MacGyvering: While this a given with most things for Donnie, here he manages to perfect his very first batch of retromutagen using chemicals found at his High School chem-lab. His inner-city public High School chem-lab.
Parental Substitute: Jason practically calls Leatherhead his dad when he tells Jason that he can still live with him and Malachi if he attends school.
Rhetorical Question Blunder: Downplayed. When Irma sarcastically asks if their (Donnie and April) next date would be on the roof of the history museum, Donnie actually considers it.
Sadistic Choice: When the freshly-mutated Baxter kidnaps April, he gives them an ultimatum: give him Donnie's retromutagen or he mutates April. Raphael and Mondo Gecko sees this as an easy option, as a few more months as mutants is a good enough sacrifice if it means saving April. In Malachi's case, he doesn't even want to be human again, finding his life much more fulfilling as he is.
Shout-Out: At the start of the chapter, Baxter deliberately quotes Wreck-It Ralph to describe himself.
So all in all, he, Baxter Stockman, (to quote Wreck-It Ralph) was a bad guy, but he was not a bad guy (end quote) who in anyway deserved the treatment he was getting.
Stupid Sacrifice: With the reveal that April is immune to mutagen, the Hamatos willing to give up their retromutagen in exchange for her, Michelangelo getting mutated andRaphael getting mutated look like this retroactively. April dissuades them on both counts, as at both points none of them knew she was immune, and in the latter her father could have been mutated like in canon, so Raphael's sacrifice was not for nothing.
Villain Has a Point: While Rahzar mocks Baxter for his failures, Baxter retorts that as least he manages to contribute his skills meaningfully (like in maintaining their Foot-Bots) while Rahzar has done nothing but fight and lose to kids with nothing to show for it. It doesn't stop the Shredder from making an example of him.
Wham Episode: In trying to rescue April from the vat of mutagen, Mikey mutates into a mutant turtle like Raphael.
