Sydney Bristow discovers that her job as an agent for SD-6, a top-secret division of the CIA, is not what she thought it was. Sydney's father, Jack, also tells her the truth about his work and she, enraged, seeks help from real CIA and is hired as their double agent under the command of Agent Vaughn. From now on, her job is really simple: she needs to complete her cases at SD-6 while reporting her findings back to the CIA.
On her first mission as a double agent, Sydney is sent to Moscow to retrieve some stolen files about nuclear bomb. Meanwhile, Will continues to grow obsessed with Danny's death and starts his own investigation even though Sydney asked him not to.
Sydney is sent to Madrid to retrieve a 500-year-old sketch that contains a set of numbers and meets up with her deadly nemesis, K-Directorate agent, Anna Espinosa. Meanwhile, Will digs deeper into the cause of Danny's death and finds some odd information.
Sydney and Dixon are sent on a dangerous case involving the safety of the United Commerce Organization. Francie gets suspicious about Charlie and spies on him. Meanwhile, Will continues to investigate the truth about Danny's murder.
Sydney's cover in SD-6 is put in danger after smuggling a wrong biotech engineer into SD-6 from her mission in Berlin. Meanwhile, Will's investigation into Danny's murder leads him to a woman named Kate Jones, who may have information about the killing. Sydney's starts to doubt where her father's true allegiances lie.
Sydney goes undercover in a mental institution to meet a guy programmed to be an assassin. Meanwhile, back home in LA, Will discovers the true identity of "Kate Jones" and Francie learns the truth about Charlie.
Trapped in the Romanian asylum run by the Russian spy group, K-Directorate, Sydney befriends amnesiac agent Mark Shephard. Sloane and Alliance representative Alain Christophe come to conclusion that SD-6 has mole(s) and plan a trap.
Sydney must undergo an extensive lie detector test to prove her loyalty to SD-6 while at the same time she is trying to find connection between a 500 year old Rambaldi sketch and a machine. In the meantime, Will gets deeper into the secrets while investigating Danny's death.
Sydney's life and cover as a double agent is placed in mortal danger when Sloane starts assuming that she is the mole. Dixon's life is at stake after the mission that went wrong. Meanwhile, Will realizes that his investigation of Kate Jones may be more dangerous than he thinks after he gets a call from the person "on the other side" of her pin.
After she manages to escape a certain death at SD-6 and still manages to maintain her cover as double agent, Sydney is sent on a private island to find new identity of Ineni Hassan, an ex weapon smuggler and previous head of weapons resources of SD-6. Things go south for Sydney after she discovers that Jack got into trouble on a mission in Cuba and in meantime, Will Tippin now focused his investigation on SD-6 whose name he heard for the first time thanks to bug from Eloise Kurtz.