Baxter Stockman's laboratory first appeared as an empty warehouse in I Think His Name is Baxter Stockman. Since then Baxter has updated it several times. Later on, his laboratory was moved to the Foot Clan Headquarters and updated with technology from the Kraang.
- Mousers Attack! - Baxter built a M.O.U.S.E.R.S. assembly line in the warehouse.
- Baxter's Gambit - Baxter turned his former hideout into a deadly maze as a way to get revenge on the Turtles, Dogpound, and Fishface.
- Mikey Gets Shellacne - The warehouse now is equipped with a tank of mutagen and Kraang technology he stole from the ruins of TCRI.
- The Lonely Mutation of Baxter Stockman - After creating 74 useless mutants for Shredder (including Ace Duck), Baxter gets mutated into a mutant fly as punishment and after suggesting making an army of mutant pigs and rhinos. This location was where it was revealed that April O'Neil was unaffected by the mutagen when she was dropped into the mutagen tank
- Vengeance is Mine - Shredder uses Karai as bait to lure the turtles to Stockman-Fly's lab and turn them into mindless snakes upon falling into the mutagen tank (which Stockman-Fly filled with snake DNA) only for Karai to accidentally get mutated into a mutant snake. In the end, the warehouse was destroyed by the fire as the effect of the resulting battle.
- Return to New York - The new laboratory was built beneath the Foot Clan Headquarters, and was updated with several habitats for storing mutants, a more refined mutation device (which contains a mutagen tank where different DNA samples can be placed into it), a Choco-Log vending machine, and Baxter's control panel from Baxter's Gambit. The Shredder Mutants were the guards of this laboratory until they were slain by the giant fan below upon being defeated by Splinter.
- Serpent Hunt - Baxter uses the mutation device to mutate Anton Zeck and Ivan Steranko into Bebop and Rocksteady under Shredder's orders.