Sydney Bristow was recruited as an undergrad to work for SD-6, which she thought was a government agency. However, when her fiancé is killed by SD-6 agents, she finds out that SD-6 is actually a counter-government agency. Sydney approaches the CIA and becomes a double agent, which means that she goes on SD-6 missions, but passes the information about her missions to her CIA handler, Vaughn.

Sydney's father, Jack Bristow, is also an double agent. Both had a distant relationship for years, but their present situation brings them closer together. Sydney and her father spend the first season trying to foil SD-6's missions and preventing them from getting their hands on what they are determined to get. For years SD-6 has fought against FTL and K-Directorate, two crime organizations that are also in the pursue of various artifacts build by the 15th century scientist and prophet, Milo Rambaldi. However, when a new player referred to as "The Man" comes to town, FTL and K-Directorate are put out of business and SD-6 engages in the pursue of this new mysterious opponent.

After eliminating SD-6 and all of the other SD cells, Sydney, Marshall, Dixon, Jack, and Vaughn are now fully working for the CIA.