Call-Back: When Raph attacks a giant cockroach and it spews fluid all over him, he mentions Bishop's aliens in "Aliens Among Us"
Didn't See That Coming: Stockman admits that the alien clones' genetics were more potent than expected, as was how hard the Turtles fought them off. The leftover genetic material entered the sewers and mutated the local animals.
"It was impossible to anticipate."
Discussed Trope: Mikey mentions that creepy voices/glowing eyes in the shadows is "never good" in monster movies
Even Evil Has Standards: While he is the one who started the fake alien invasion, Bishop is not really pleased at finding out about the outbreak.
"Doctor, my life's work is to defend humanity from extraterrestrial threat, and now you're telling me that I've unleashed this-this plague?!"
Foreshadowing: During the fight, the mutated sewer worker hits Donatello with one of its spiky tendrils. For the next several episodes, Donny will wear a bandage and feel progressively worse until he mutates into a monster.
While Donny and Mikey collect raw materials, Leo and Raph stand guard for any Foot Ninjas that might come passing by, which does occur. Leo also says they'll eventually deal with the Foot, but on their terms—not Karai's.
When Stockman shows him pictures of mutated animals, Bishop immediately suspects these are the result of their phony invasion.
The Greys: Bishop's abductors in the opening narration
The Law of Conservation of Detail: The Turtles get beaten and injured all the time, but we rarely see them bandaged or wounded unless its after a big fight. So when Don is scratched by the mutant bug, and the camera makes sure the audience sees it, you can be sure that little scratch will be an important plot point later...