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 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.
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.
After the SD-6 finds out that another terrorist organisation was attacked at the same time as them, Sydney and Dixon are sent to Las Vegas, and later Moscow, to try to find something that will bring SD-6 closer to identity of The Man. All in the same time, Sydney learns some shocking news about Francie's fiancé, Jack tries to be a better father to Sydney and Will begins his journey in discovering SD-6.
Vaughn presents Sydney with a moral dilemma that includes Sloane's ill wife, Emily, in order to fulfill the mission whose outcome is an unpleasant surprise to everyone. SD-6 goes after Will when he comes too close. Meanwhile, Francie is dealing with her broken heart.
Department of Special Research gained interest in Sydney's role involving the page 47 and they began their own investigation regarding it. To save herself, Sydney needs to steal 500 year old Rambaldi codes from Vatican to decipher Rambaldi's prophecy. Meanwhile. Sloane gets suspicious that one of the Alliance's members switched sides and is now working with The Man.
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...
After she managed to prove her innocence to FBI, Sydney is sent to Vienna to retrieve data from SD-6 spy in Russian Embassy. There she runs into Noax Hicks, her ex who broke her heart and left her without a word few years earlier. Meanwhile, Sloane promises Sydney to help her find her mother and Jack is losing his mind because of it.
As Sydney and Noah go to Cape Town to get some data on "The Man" , Sloane begins to question where Noah's true allegiances lie when his team finds some suspicious bank activities of his. Vaughn goes to Colombia to get information about Russian assassin known under the codename "Snowman" whose recent mission was to kill Kjasinau, a.k.a. "The Man". While Sydney is getting closer to the truth about her mother, Will and Francie confront her about the airline ticket they found in her coat.
Francie is having a rat problem in her house and gives an inspiring speech about catching them which gives Sydney idea how to catch Khasinau. She and Vaughn set up fake transaction for a Rambaldi artifact with Satk, but their job is compromised when Sloane sends SD-6 agents to steal the presumed second vial. Meanwhile, Will learns the truth about his kidnapping and Jack Bristow has no option but to help him.
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...