Malory hosts a dinner party for the UN intelligence chairman, Torvald Utne, in an effort to get a new weapons contract for ISIS. Unfortunately, a group of rival assassins have targeted Mr. Utne for elimination.
Malory's career is threatened when a sensitive videotape falls into the hands of a rogue (and roguish) Cuban agent, so she calls on Archer's expertise in seduction to turn the tables on her blackmailer.
Archer must rescue Lana from the clutches of Skorpio, the infamous arms dealer. Meanwhile, Cyril fears not only for his girlfriend's life, but her succumbing to the seductive nature of Archer's heroics.
Barry extends an employment offer to Lana after seeing some of her actions in Paris. However, due to a misunderstanding, Sterling believes the offer was give to him. Archer then takes a higher-paying job at ODIN and Malory will stop at nothing to get him back.
In yet another attempt to secure funding for ISIS, Malory drags her agents to the luxury winter resort town of Gstaad to protect a German billionaire's daughter from a kidnapping threat. But Archer soon finds out the real threat is his protectee: an underage nymphomaniac who will stop at nothing to bed the world's greatest spy.
After Malory is wiped out in a Ponzi scheme, she hatches a scheme of her own: selling ISIS - lock, stock and snack machines - to archrival spy agency ODIN. Archer and the rest of the ISIS employees, rightfully fearing for their jobs, must use every trick in the book (ISIS Field Manual, 3rd Edition) to try to stop the sale.
Trinette tries to accuse Archer as to being the father of her baby son, Seamus. Archer tries as much as he can to get out of paying child support if the paternity test passes, but begins growing a bond with the child.
Tired of his colleagues constantly calling him a failure, Cyril agrees to help George Spelvin, a mysterious computer security expert, inject a pirate virus into the ISIS mainframe so Cyril can defeat the virus and be seen as a hero.
After the death of his fiance, Archer goes missing for three months. Malory sends a former agent named Rip Riley to find him and bring him back. With Archer's resistance, he ends up stranding them out at sea and mixing them up with pirates.
Archer becomes leader of a pirate island and is enjoying the high life until a disgruntled islander calls mutiny. With Archer, his first mate Noah, and Rip Riley now trapped on the island, Ray and Lana go out to look for him.
Cyril is promoted to field agent, while Malory institutes a strict drug testing policy for her employees. Neither of which sit well with the staff at ISIS. As Cyril is promoted to field agent, he accompanies Sterling and Lana to South America to collect on a bounty of $1,000,000 on Román Calzado. Ray, Cheryl, and Pam know they will not pass the drug test, so they enlist Doctor Krieger to help them pass.
Archer's sex life compromises his effectiveness as an agent. When Nikoli Jackov defects to the United States, he is accidentally killed by Archer's drunken incompetence when he fails to guard the safe house.
With Krieger operating an online pharmacy to distribute the cocaine to buyers, the gang has the free time to throw a neglected Lana a baby shower. Archer takes Pam along for backup on a trip to the Tuntmore Hotel to secure a very special shower gift: a performance by Kenny Loggins.
Archer helps Lana with the delivery of her baby, while Krieger and Ray try to prevent the launch of a deadly nerve gas rocket. Cyril is dethroned as 'leader' of San Marcos, Malory negotiates an underhanded deal with the CIA to reactivate ISIS, and the father of Lana's baby is finally revealed.