The title is a humorous reference to the phrase "jumping the shark," used to describe shows that have reached their peak and started to decline in quality. Chris Carter said that the title was tongue-in-cheek, and that it was their "way of lowering the boom on anybody who thought that it did."
The X-Files spinoff "The Lone Gunmen" had only one season of 12 episodes. It ended with a cliffhanger as Chris Carter et. all. thought there would be a second season. This crossover episode wraps up many of the loose ends, and is included in the DVD set of The Lone Gunmen.