Mikey and Don drive into the river in The Shell Sub, only to discover something terrible sitting on the river bed...
This episode provides examples of
- A Day in the Limelight: The episode is almost entirely focused on Mikey and Donnie's adventure, with the rest of the family only appearing briefly at the beginning and end.
- Animal Mecha: The giant mecha whale counts as Subtype 1.
- Atlantis: Briefly mentioned by Don and Mikey when they sight the underwater base. In addition, the name of the episode is a composite of 'junk' and 'Atlantis'Donatello: Atlantis is a myth, and even if it isn't, I don't think it's a suburb of New York.
- The Bus Came Back: The Garbageman returns from Season 1 after being knocked into the ocean.
- Dead Hat Shot: Done with the nameless boat captain at the beginning.
- Good Old Fisticuffs: Neither Mikey nor Donnie brought their weapons on what they assumed would be a peaceful exploration of the river from inside the Shell Sub, forcing them to fight hand-to-hand or use improvised weapons against the Garbageman and his mooks. It doesn't slow them down much.
- Mugged for Disguise: Mikey and Don do this to a couple of mooks.
- Oh, No... Not Again!: The Garbageman, as he sinks down into the underwater trench at the end of the episode.
- Sarcasm Mode: When Splinter is splashed by river water, he says "Just what I needed; another bath."
- Shout-Out: Mikey asks Don "Aren't you a little short for a junk trooper?" Later he also says "To the Shell Sub, Boy Wonder."
- Title Drop: After getting a better look at the Garbageman's underwater city, Mikey comments, "That's not Atlantis. It's Junklantis."
- Underwater Base: The Garbageman's new base of operations.
