He first appears in the first arcade game, as a boss in the Sewer, flying a hovering machine and dropping Mousers. Baxter does not attack the Turtles directly, but the sheer number of Mousers that he can produce keeps the player on his or her toes. He is in his human form during this battle.
In the NES port of this game, Baxter in his fly mutation replaces the Bebop and Rocksteady dual-boss fight from the arcade version. He flies around with an energy gun and a fly swatter and attempts to subdue the Turtles whilst April O'Neil sits tied up in the background. The NES instruction manual calls him Knat Man to differentiate between the forms - a name which has caught on as a catch-all term within the fandom to refer to his fly form.
Baxter Stockman also appeared as a boss in his mutant fly form in the Game Boy games Teenage Mutant Ninja Turtles: Fall of the Foot Clan and Teenage Mutant Ninja Turtles II: Back from the Sewers. Baxter the Fly appears as an enemy in the handheld game Teenage Mutant Ninja Turtles 3: Shredder's Last Stand. In the game he flies above the battlefield and can only be hit by Shurikens.
Baxter Stockman appears in his mutant fly form as the first boss in both the Arcade and SNES versions of Teenage Mutant Ninja Turtles: Turtles in Time. He resumed his role as the first boss in the Re-Shelled remake for Xbox Live and PlayStation Network, again appearing as a fly mutant and voiced by Sam Regal.
In Teenage Mutant Ninja Turtles: The Manhattan Missions Baxter appears in his human form in his lab while you fight Usub Gerstalk.
Baxter found his way back to his human form for Teenage Mutant Ninja Turtles: The Hyperstone Heist, emerging as the final fight for The Gauntlet, behaving much as he did in the original arcade game.