Blood Knight: When the Hamatos theorize how they could get ahold of mutagen to cure the mutated humans, Miwa comes up with the idea of gutting a Kraathatragon.
Leo: Sis, [s]ometimes you scare me. Donnie: Only sometimes?
Call-Back: When Mikey asks why he can't be the one giving orders while in Dimension X, Leo rhetorically asks "Am I covered in mutagen zits?" before making it clear that he's still team-leader.
Shout-Out: When everyone makes it to Dimension X, Metalhead briefly plays The X-Files theme song.
Raphael: So to sum it up, [w]e're in another Dimension, trying to do the impossible and save all the people of New York, and riding in a ship piloted by a Donnie's crazy robot who can only drive like he's in a car chase. Miwa: If anyone's next words are along the lines of, "It can't it get any worse," I can't be held responsible for my actions.
Later invoked.
Raphael: We made it, Wow, that was easy. [Miwa smacks Raph upside the head] Miwa: What did I say about saying things like that.
Wham Episode: The Kraang Invasion has been fully reverse with all of the kidnapped, mutated demons returned to New York and the Hamatos have enough retromutagen to cure themselves.