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 to crash a plane into the World Trade Center.

The Lone Gunmen are trying to find out who killed a fellow hacker. In the midst of their adventures they meet a not-so-bright football player named Jimmy Bond.

Frohike goes deep undercover as a long lost son, after the Gunmen receive a tip which could lead them to a female baker who poisoned members of the French Resistance back in the second World War.

The Lone Gunmen and Jimmy are trying to find the long lost "water powered" car that Frohike saw with his own eyes back in 1962. Only, they are not the only ones who are after it.

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.

Jimmy and Byers are jailing themselves into a high security jail so they can get access to a death row inmate who is potentially innocent.

While the Lone Gunmen stalk an illegal grizzly-bear trader in a snowy forest, an injured Jimmy believes his doctor is a serial killer.

Yves becomes a smuggler's partner in a tango competition in Miami while the Lone Gunmen are afoot to uncover what Yves is after.

The Lone Gunmen are surprised to find that FBI's Walter Skinner is somehow involved in the murder of Byers' old college roommate who tried to blackmail a gangster with ties to Russian mafia.

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.

In the series finale, the Gunmen team up with Morris Fletcher, the sleazy Man in Black from Dreamland (1998), to find the person who stole the list of false flag operations. The cliffhanger ending is resolved in Jump the Shark (2002).