For Want Of A Nail: In "The Mutation Situation", April and the turtles lie to Kirby about the purpose of the sonar devices because of how paranoid he is of the Kraang. Here, they are more forthcoming about it, leading to him agreeing on the condition that Raphael stand guard. This results in Raphael getting mutated instead of Kirby, turning into a mutant turtle.
Foreshadowing: Mondo Gecko, Sir Malachi, Mushroom Man, Pizza Face and the Squirrelanoid's mutations are briefly mentioned.
Heroic BSoD: Raphael's mutation was so traumatic that the first thing he does once his mutation finishes is to hide in his shell until his siblings arrive.
Mythology Gag: The various "mutant names" Mikey tries giving Raphael include Terrorpin, Shellshocker, Slash, Turtle Titan, Nightwatcher, Franklin, Griddex and Snapper McTortoise.
Stating the Simple Solution: When asked why he picked Raphael to be his body guard, Kirby admitted that it was by process of elimination; while Raphael is a good enough solo fighter to act as a body-guard, Leonardo is needed to coordinate the team, Michelangelo is too flighty to be trusted with protecting them, Donatello is needed for his genius for the delicate tech on the mission (not to mention being worried that he would get too distracted by April), Leatherhead intimidates him and Miwa just outright terrifies him.
Taking the Bullet: Raphael gets covered in a canister of mutagen that would have fallen on April and Kirby.
Wham Episode: Raphael gets mutated into a mutant-turtle.
