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
- 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'
- 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.
- Mugged for Disguise: Mikey and Don do this to a couple of mooks.
- 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."
- Underwater Base: The Garbageman's new base of operations.