"Kill the Alligator and Run" was written by John Swartzwelder and directed by Jen Kamerman as part of the eleventh season of "The Simpsons" (1999–2000). When the animation department finished its work on the episode, it had ended up being about four minutes too long and the staff of the show was forced to make some difficult cuts. One scene that was cut saw Captain Jack lying in state at the capitol in Florida, with Kid Rock being one of the people present to pay their respects to the alligator. "The Simpsons" showrunner Mike Scully has expressed regret for cutting this scene because it "hurts the logic" later in the episode when Captain Jack crawls out of the capitol and reveals himself to everyone, thus creating a plot hole due to a lack of any explanation as to how he got there.