Raphael paints a green woman with a red mask with the name "Venus" next to her on the Party Wagon. Venus was a female Mutant Turtle from Ninja Turtles: The Next Mutation (1997).
This is the second appearance of the Party Wagon, the Turtles' vehicle from Teenage Mutant Ninja Turtles (1987).
The bomb the turtles throw from the Party Wagon was taken from the Teenage Mutant Ninja Turtles (1987) toy. The bomb reads "Foot stinks", the same slogan written on the 1987 Party Wagon.
The Shredder Mutants are inspired by the clones of the Shredder from the Mirage TMNT comics.
One of Donnie's ideas for a new lair is an old subway station. This was seen in Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991).