The Lone Gunmen investigate the suspicious death of Byers' father, a top tier government agent, and discover a top secret plan for a false flag operation eerily similar to the real life event colloquially known as 9/11.
A baby is introduced in the lives of the Lone Gunmen as a link between a popular senator running a campaign for re-election who was involved with one of his campaign workers who died in a very suspicious accident.
The guys are approached by a desperate man in need of help who claims to have apparently been erased from existence. The Gunmen's only clue to this mystery is the man's inexplicable hate for a specific late midget wrestler.
The Gunmen receive an email for help from a 'slave' subjected to secret government tests. The slave turns out to be a superintelligent chimp called Peanuts, who escapes supposedly to stop a soviet chimp spy turned assassin for hire, Bobo.
In the series finale, the Gunmen team up with Morris Fletcher, the sleazy Man in Black from X-Files: Dreamland, to find the person who stole the list of false flag operations. The cliffhanger ending is resolved in X-Files: Jump the Shark.
Cap'n Toby, the host of a long-running children's show and Langly's childhood hero, is accused of spying for the Chinese. The gang investigates the so-called Rose-Colored Glasses Lady, a dangerous operative who may know more.