Archer is still reeling from the death of his fiancée by taking a siesta to an island in the South Pacific. Malory, needing Archer back, sends noted adventurer Rick Riley to retrieve Archer and escort him back to Isis. Archer refuses until he's dragged out.
Archer finally agrees to head back to Isis. Unfortunately as he boards Riley's plane to head back, their plane is attacked by pirates and they soon find themselves on an island run by pirates, and Archer is crowned their new pirate king.
Malory finally sends Lana and Ray to get Archer back. But Archer has quickly settled into his new role as king of the pirates. But Archer and Rick soon go from leading the pirates to being their prisoner, and Malory must negotiate for Archer's freedom.
Archer is stunned to learn that his mother is dating his man crush - Burt Reynolds. As Archer and Burt bond, they soon discover that they have more in common than once thought, while Archer has to defend the rest of the crew after his carelessness gets them in trouble with a ruthless gang of Cuban drug lords.
Cyril is promoted to field agent just as the Isis crew is called to bring in the bounty on a South American drug lord - Armando Calzado. But Cyril's incompetence gets him lost and Archer and Lana thrown in jail and they have become a target for Calzado to hunt. Meanwhile, the rest of the Isis crew is ordered by Malory to take a drug test, and uses an experimental detox cure from Krieger with predictably disastrous results.
The Isis crew is ordered to transport a dangerous terrorist across the border to Canada. A drunken Archer wants to fulfill his lifelong dream of fighting a bunch of random guys on the top of a speeding train. Meanwhile, the rest of the Isis crew boards against Malory's orders on Cheryl's private cars.
For Archer's birthday, Malory and the Isis crew surprise him with a souped up Dodge Challenger, complete with all the latest high tech gear. Unfortunately Archer turns his back for one second and the car's gone. Archer and Lana soon head to the underground of New York City's street racing scene to get the car back.
Archer and Lana are called over to Malory's apartment on what was supposed to be an off night for the Isis crew. There, they are shocked to discover what appears to be a dead body, some foreplay, and a few random gun shots. As they put together the pieces of the mystery, they soon discover that there's more to this story than meets the eye, and does Archer have enough spaghetti and meatballs for everybody? And what is underneath Malory's trench coat?
The Isis crew travels to West Virginia to help Ray and his brother save their crop from a crooked Sheriff. Meanwhile, Archer discovers that Ray has been faking his paralysis.
After a wild night involving Archer hitting on the widow of a deceased Isis agent and some heavy drinking, Archer wakes up in his apartment to discover that he's had the best sex of his life. Unfortunately, who he discovers that it was with jeopardizes his ability to perform on the job.
When Archer's fiancée returns under mysterious circumstances, he immediately suspects that his arch rival Barry is behind it, and soon begins to plot against them both.
The Isis staff is called by NASA to stop the international space station from being taken over by space pirates. During training, Cyril proves to be a more than adequate pilot, while Malory attempts to make drinks in low gravity, and Lana has an unusually weak stomach.
Once on board the international space station, Archer and the Isis crew have very little time to save the crew on board from being taken over by space pirates, but an even sinister motive looks to make things even worse for Archer and Isis.