Adaptational Context Change: In "Mazes And Mutants", the turtles didn't know anything about Malachi until he trapped them in his maze, having stumbled upon him in a LARPing session. Here the Hamato Kids were actually looking for him, Martin being on Casey's list of missing kids when the mutagen was spread over the city.
Ascended Extra: While Malachi only appears in one episode, here he joins Mondo Gecko and Leatherhead as "another stray" mutant.
Brick Joke: At the start of the chapter, Miwa jokingly compares Raphael to a Disney Princess for his affinity for animals. Later, Malachi makes him the "captured princess" when he demands that if he's going to be stuck playing his game, he gets a different role outside of being a hobbit.
In canon, the turtles were the only ones forced into Malachi's game, with illusions of Rockwell, April and Leatherhead being used as glorified props for the game. Here Casey, April and Miwa are also involved, the costumes he put them in being a ranger, a pirate and a thief respectively.
In canon, the turtles were only dressed in their LARPing gear, having worn it before Malachi got to them. Here their costumes are much more authentic looking, Malachi having conjured it for them.
Mistaken for Own Murderer: At some point, Raphael interrogates Malachi on whether or not he was the one who kidnapped Martin, unaware that he is Martin.
Mythology Gag: Raph sarcastically asks Malachi if he'll give him a turkey-head if he doesn't cooperate, something he actually does in-canon.
Schmuck Bait: At the beginning of this chapter, it is acknowledged that Mondo Gecko finding a perfectly pristine Tabletop RPG set just lying there in the sewer is mildly suspicious.
