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 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 Dreamland (1998), to find the person who stole the list of false flag operations. The cliffhanger ending is resolved in Jump the Shark (2002).