Donatello is working hard in order to make an antidote for the people living in the underground city.

----
!!This episode provides examples of:

* AllWebbedUp: Happens all of them except for Donatello, who took the tunneler under the lava to get the crystal moon.
* AllWorkVsAllPlay: In the beginning of the episode, Don is all work while Leo, Raph, and Mikey are all play.
* TheBerserker: All of the monsters, this time.
* CallBack:
** Quarry told the turtles that she and her companions would eventually be stripped of their intelligence and thought and become savages just like the other test subjects. In this episode it has come to pass, and she, Razor Fist and Stonebiter mindlessly attack the turtles.
** Mikey says that Don had a "crystal dream" [[Recap/TeenageMutantNinjaTurtles2003S1E13NotesFromTheUndergroundPart1 like the one he had]].
* ContinuityNod: In "Notes from the Underground Part 2" Quarry could only remember that her real name began with an S. Here we find out what it really is.
* ConvectionSchmonvection: As before, the turtles stand right next to a lake of lava with no ill effects. The spider mutant also shrugs off falling into the lava.
* DreamingOfThingsToCome: in his dream Don is cryptically told by Quarry how to develop a cure for the people in the underground city
* DrillTank: The Turtle Tunneler
* {{Foreshadowing}}: This episode hints the The Entity wasn't being completely honest about his backstory in Part 3 of the "Notes From the Underground" arc as we see a room with figures suspended in animation just like him, his true nature would be revealed in "The Entity Below"
* GivenNameReveal: [[spoiler:Quarry's real name is Sydney]].
* IKnowYoureInThereSomewhereFight: [[spoiler:Mikey tries this one on Quarry, but it fails]].
* IntelligenceEqualsIsolation: At the start of the episode Don's sequestered off in his lab, trying to find a cure for their friends in the underground city.
* LastOfHisKind: The "Sole Survivor" from the last time was lying about his people being extinct.
* LavaIsBoilingKoolAid
* MyFriendsAndZoidberg: Don presents the Turtle Tunneler to his brothers this way.
-->'''Don:''' Gentlemen, [[AnnoyingYoungerSibling and Mikey]], I give you the Turtle Tunneler!
* OOCIsSeriousBusiness: The normally-mild Donnie yelling and snapping at his brothers indicates that he's been overworking himself and is exhausted. {{Lampshaded}} by Raph, who points out that Donnie hasn't slept in days.
* TearsOfJoy: Quarry after returning to the surface as a human.
----