The source of the mysterious crystals found in the lair appears to be an ancient subterranean city. This site is also the location where Donatello and the Turtles' monster allies disappear. The city is inhabited by the sole survivor of an ancient race; although he claims wanting to return the creatures to their original form, his true intentions remain unknown.
This episode provides examples of:
- Bittersweet Ending: The humans can't stray too far from the city without mutating, but at least they can find a way to permanently reverse their transformations.
- Dwindling Party: A non-lethal version, and an obvious shout-out to the common monster movie trope. The turtles and the friendly monsters all slowly disappear, one by one, until only Michelangelo is left. He reunites with them all, though.
- Naked on Revival: Quarry as a human again. Much to the Turtles' surprise.
- Samus Is a Girl: Quarry.
- Well-Intentioned Extremist: The Sole-Survivor. He wants to help the mutant people return to their human forms, but only so they'll stay in the underground city and repopulate it.
- You Gotta Have Blue Hair: Quarry, in both mutant and human form.