ISIS agents head 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.
Broke after having been wiped out in a Ponzi scheme, Malory decides to sell ISIS to rival spy agency ODIN, whose chief happens to be in love with her. Not surprisingly, the ISIS staff tries to stop the sale---and the romance.
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.
Some other changes were noticed by fans of the show. One of the most notable being Archer's skills as the "world's most dangerous spy." In Season 1, his skills as a spy were not showcased very often, so many fans believed he lacked many of the skills. This was proven otherwise with this season's first episode, "Swiss Miss." Here Archer had many opportunities to show that he was a fairly capable field agent.
This season increased the show's focus on the Archer supporting cast. This included adding more frequent appearances by the character of Ray Gillette. Instead of being chained to the ISIS control room, he has now been able to get out and about as an ISIS field agent. Also, details about the backstories of Pam, Cheryl and Doctor Krieger were revealed.
Furthermore, this season saw the addition of numerous two-part episodes. These were episodes in which the broad story was told over two episodes. They didn't follow the traditional television model of adding a "to be continued" tag at the end, but they did end "Stage Two" and "White Nights" on somewhat dramatic cliffhangers.
On a side note, every episode of the second season starts with a character's face at least partially obscured by the TV rating box in the upper left corner of the screen. This was done on purpose by the creator as a protest to a previous accidental incident in which they refused to move the box.