After the Foot Clan destroyed their sewer home in the first movie, the Turtles and Splinter spent some weeks with April O'Neil in her new apartment. However, this was problematic for all the parties involved, as the apartment was not meant to house six people, and Splinter deemed it to be time for them to find a new underground lair.
The Turtles began scouting sewer tunnels for a new lair, though Raphael almost immediately left to pursue the Foot. Michelangelo fell through a shaft in the floor, discovering himself in an abandoned train station with a stopped car, and called for Donatello and Leonardo to follow him. Despite Michelangelo's apprehension at the dust and spiderwebs, they began moving in and cleaning up immediately.
- This location was inspired by a real closed New York City Subway station called City Hall Station, which shut down in 1945.
- The film's actual subway and shaft sets were built and filmed at Screen Gems in Wilmington, North Carolina, and were later reused in Teenage Mutant Ninja Turtles III and then moved to Vancouver, BC for the short-lived Fox Kids TV series, Ninja Turtles: The Next Mutation.
- Original production used 29.5" x 41.5" subway shaft plan dyeline blueprints from Teenage Mutant Ninja Turtles II: The Secret of the Ooze. Dyeline blueprints such as this would have been handed out to the art department and set construction crew. The blueprint label reads as follows: "PRODUCTION DESIGNER: ROY FORGE SMITH / SET: SUBWAY SHAFT / LOCATION: STAGE 1 / DRAWING: SUBWAY SHAFT PLAN, ELEVATION, SECTION / DATE: 8-13-90 / SCALE: ½" = 1'0" / DRAWN BY: G.S.G. / SET: #17 / PAGE: #1701."
- The blueprint shows detailed layouts of the interior of the subway shaft and the sidewalk vents where pedestrians would walk overhead.
- Roy Forge Smith was the production designer on all three live-action Ninja Turtle films, as well as on Monty Python and the Holy Grail and Bill & Ted's Excellent Adventure.
- "G.S.G." are the initials of Geoffrey S. Grimsman, who's credited for being an art director on the film. Grimsman was also a set designer on Super Mario Bros. and the assistant art director on The Crow.