The third season of Archer consists of 13 episodes. FX aired the first three episodes in September 2011 which followed Sterling's actions after the finale of the second season. The remainder of season 3 continued airing on January 19, 2012. Notable guest actors signed on for the season include Burt Reynolds playing himself as Malory Archer's love interest, Michael Rooker as Sheriff E.Z. Ponder and Bryan Cranston as Commander Drake in the two-part season finale.
The season was initially ordered for sixteen episodes, but Adam Reed mistook the order for the first three episodes in September as part of a 13-episode order.
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.
One alternate version of the Season 3 DVD cover features an image of Malory sitting cross-legged holding a cigarette and an empty cocktail glass. This pose is directly inspired from an image by acclaimed illustrator Robert E. McGinnis for the pulp noir Kill Now, Play Later.
The alternate cover also features Cyril Figgis in an outfit similar to Naked Snake (Big Boss) from the game Metal Gear Solid 3 Snake Eater, an extremely capable field agent, which is opposite of what Cyril is in the show.