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.
After she and Shepard escape from the asylum in Romania, Sydney discovers his connection with her past. Sloane and Alliance representative Alain Christophe come to conclusion that SD-6 has mole(s) and they start a search.
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 places 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.
Sydney is sent to Greece to retrieve information about new weapons that are being produced by a young tycoon. Meanwhile, Vaughn plans to report Jack for his apparent involvement in murders of many CIA agents and by doing so, he crushes Sydney's newly found admiration for her father.
When former SD-6 agent McKenas Cole with his crew of bandits take over SD-6, Sydney has to forget her previous plan about quitting the agency and has to focus on her mission with Jack to save their colleagues. In the meantime, as he was about to quit his work on a story, Will Tippin gets an unexpected push to continue from the third party.
Vaughn disobeys the CIA in order to infiltrate SD-6 when he receives a desperate plea for help from Dixon. At SD-6, Cole continues his vendetta against Sloane and his search for device in possession of SD-6. Elsewhere, Will continues his work on story.
Sydney and Dixon are sent to Las Vegas to gather information from a K-Directorate agent who has ties to the McKennis Cole group that attacked and nearly destroyed SD-6. Meanwhile, Sydney learns some shocking news about Francie's fiancé, Charlie, and tries to stop them from getting married, all in the same time. Back in Los Angeles, Will begins his journey in discovering what SD-6 really is, and Jack continues to try to be more of a father to Sydney when he helps her decide whether or not to continue with graduate school.
After escaping a near accident in Moscow after getting a tip about "The Man" from K-Directorate, Sydney must go with Dixon to snatch the Rambaldi book stolen in Argentina on the coasts of Tunisia. Will Tippin is forced by some mystery men to abandon his investigation about SD-6. Sydney is invited to Sloane's house, with Jack and Will, but must do a secret mission for Michael about a special "page" which might shock her...
The SDR section of the CIA is getting interested about Sydney's picture on the Rambaldi's page and starts to question her. In the meanwhile, Sloane discovers who is "The Man", and consults one of the Alliance's members, Edward Poole, who gives proof that one of the members does finance his activities in a eve of an Alliance council in London. Sydney must go to Rome with Michael to get a Rambaldi secret from the Vatican secret vaults.
Sydney is heavily questioned by the FBI concerning her past and her current activities at SD-6. Fearing that the FBI might detain her longer, Jack and Vaughn must find a way to make her escape before she blows her cover with SD-6...
Jack and Vaughn managed to get Sydney out of the FBI claws via a diversion. However, she and Dixon must go to Vienna to retrieve some data from the Russian Embassy in order to retrace the Man known as Kasinov. However, Sydney finds an old flame when on this mission. She embarks with him again in Siberia to get a device which can get clues to get closer to the SD-6 arch enemy...
While Vaughn goes to Colombia to get information about a possible killer called Snowman, who attempted to kill Kasinov, Sydney and Noah go to Cape Town to get data on some bank transfers "the Man" made for its activities. Back at SD-6, Sloane investigates Noah, finding some other suspicious activities... Finally, Sydney gets a clue to find out where her mother is, and gets to Australia where she is in for a surprise...
In order to catch Khasinau and get closer to finding her mother, Sydney and Vaughn set up an undercover transaction for a Rambaldi artifact with Khasinau's representative, Mr. Sark. But Sydney's cover may be compromised when a SD-6 agent is sent in to thwart the sale: that being Dixon himself. Meanwhile, Will is enticed by his unseen source to continue his investigation of SD-6 when he learns that Jack Bristow was one of his kidnappers. Also, Sloan's cancer-stricken wife, Emily, tells Sydney that she knows about SD-6, which forces Sloane to make the most difficult ...
Will's life is about to change as he is sent to find the person responsible for leaking information to him about SD-6 in which requests that he travel to Paris, France. Meanwhile, Sloane finds himself on the edge of finally tracking down Khasinau when SD-6 captures "The Man's" right-hand man, Mr. Sark. Also, Dixon becomes suspicious of Sydney's activities and thinks about reporting her to Sloan despite knowing that SD-6 will have her killed as well.
Sloane must take a difficult decision in order to get to the Alliance's council. After being captured by Sark, Tippin is tortured by a Taiwanese would-be dentist to extract secrets. Sydney, who has to beware her colleague Dixon, assist her father trying to save Tippin. However, after losing Vaughn when the lab exploded, she is in for a surprise...