When Sydney finds out the secrets about SD-6, a division of the CIA, she decides it's best that she tell the man she will soon be marrying, Danny, who gets killed because of it. Then she decides that she needs to stop SD-6 and enlists in the real CIA, like her father. She becomes a double agent, under the eye of her handler, Vaughn. Now her mission is to pretend to be faithful to SD-6, but secretly give information to the CIA.

When Sydney returns to SD-6, she is assigned to go to Moscow to retrieve some files, with co-worker Dixon. But things go wrong when she realizes that she has given SD-6 access to nuclear weapons, she has to go to Cairo to fix it. Meanwhile, Will starts to become curious about Danny's death. Also, Sydney finds out her father's role in Danny's death.

Sydney's life becomes in danger when she goes to Madrid to find a 500 year old sketch, and runs into enemy Anna Esponosa, K-Directorate. Meanwhile, Will is still searching on the cause of Danny's death, and finds odd information.

Dixon and Sydney go on a mission to ensure the safety of the United Commerce Organization. Meanwhile, Will becomes closer to the mystery of Danny's death. Also, Francie confrots Charlie about his date with another woman.

Sydney's cover as a double agent is put in harms way after taking engineer to SD-6 from her mission in Berlin. Meanwhile, Will meets a woman who claims to have had an affair with Danny. Also, Vaughn tells Sydney that her father may be working for another agency.

Sydney goes undercover as a mental patient to meet a guy programed to be an assassin. Meanwhile, Will finds the true identity of the woman who says she had an affair with Danny, and Francie learns that Charlie did not have an affair. Also, Sydney believes that her father killed her mother 20 years ago, and Marshall finds the bug planted by the CIA in SD-6's mainframe.

Sydney learns about the Shepard's involvment in her past. Meanwhile, Sloane confronts the Alliance about the CIA bug, and they come to the conclusion that SD-6 has been moled. Also, Will continues his investigation on the woman who had an affair with Danny and Sydney finds out her father's true involvement with her mother's death.

Sydney has to undergo a lie detector test, from Sloane, who is looking for the SD-6 mole. Meanwhile, Sydney goes searching for the connection between a 500 year old Rambaldi sketch and a machine, with Anna Espinosa on her tail. Also, Will is still looking for the mystery behind Kate Jones, Danny's so called mistress. And Sydney discovers a keepsake owned by her mother, which deepens her into her father's past.

Sydney's life and cover as a double agent is put at risk when Sloane is told that Sydney is the SD-6 mole. Meanwhile, Dixon's life is at stake after he is shot during a mission. Also, Will's investigation of ate Jones reveals some unexpected things.

Jack has to save Sydney after Sloane ordered for her to be tortured and killed after she is suspected as the SD-6 mole. Meanwhile, Sydney tells Vaughn about her recent time at SD-6, but comes to shock when he gets her a Christmas present. Also, when Will is listening to a tape, he hears SD-6, and decides to do some research, which is not the best idea.

After Sydney's father saves her life during a mission in Havana, she becomes greatful and proud, but when she finds out from Vaughn that he was resposible for the deaths of many CIA agents, her feelings becomes mixed.

When former SD-6 agent, McKenas Cole takes over SD-6, Sydney and Jack must work together to save their co-workers and Sloane. Meanwhile, Will begins to fear his decision of looking into SD-6.

Against the wishes of the CIA, Vaughn goes to SD-6 to help Sydney out. At SD-6, Cole continues his search for a device in Sloane's possession. Also, Will continues his investigation of SD-6.

Sydney and Dixon are sent to Las Vegas to get information about a K-Directorate agent who is involved with the group that attacked and almost ended SD-6. Will deepens his research about SD-6. Also, Sydney finds shocking news about Charlie, Francie's fiance.

Sydney has to use her friendship with Emily to gain access to a Rembaldi manuscript, under the request of Vaughn. Meanwhile, Will is kidnapped, and ordered to stop his investigation of SD-6 or his family and friends will pay the price.

The DSR tests Sydney to find her connection to a 500-year old picture and prophecy in a Rambaldi maunscript. Also, Sloane learns that a friend may be working for the enemy.

The FBI comes and questions Sydney about her connection to a 500-year old Rambaldi prophecy. Vaughn and Jack have to rescue Sydney, before SD-6 finds out. While Sydney is escaping, she realizes how her mother faked her death 20 years ago.

While on a mission searching for Khasinau, she runs into an ex-flame, Noah Hicks. Meanwhile, Jack has to visit Dr. Barnett after he learns that Irina may not have died, and Will and Francie suspect Sydney after they find a plane ticket stub. Also, Sydney tells Sloane, she'd like to persue finding her mother.

Sydney and Noah pick up where they left off 5-years ago, but soon Sydney begins to suspect Noah's loyalty. An assassin, Snoman, sent by K-Directorite is sent to kill Khasinau. Also, Sydney makes Jack mad when she continues to persue information about her mother, and Will and Francie confront Sydney about her mysterious activities.

Sydney and Vaughn are sent in to meet with Mr. Sark in order to catch Khasinau, but soon Sydney's cover is endangered when a SD-6 representitive is sent to stop the trade. Meanwhile, Will makes a discovery while researching SD-6 and Sloane is forced to make a tough decision after Emily tells Sydney about SD-6.

SD-6 becomes close to finding Khasinau, when they capture his assistant, Mr. Sark. Meanwhile, Will's life is endangered when he is sent to find the person who told him about SD-6. Also, Dixon becomes suspicious of Sydney's activities.

Vaughn and Sydney must destroy a Rambaldi artifact in order to save Will. Also, Jack makes a deal with Mr. Sark, and The Alliance decides the fate of Emily Sloane. Also, Vaughn's life is endangered when he gets locked in with a destroyed Rambaldi artifact, and Sydney comes face to face with Khasinau, and someone who she least expects.