Sydney finds herself face-to-face with mother. Also, Sydney becomes worried for Vaughn, for she cannot find him. Also, Will's life changes after he finds about SD-6 and Sydney's other life, and Dixon is unsure if he should tell Sloane about Sydney's suspicious behavior.

Sydney is unsure if her mother's kindness was real or was an attempt to kill her. Meanwhile Sloane is made a partner of the Alliance of Twelve, and Will sees Francie talking with a man about her restaraunt, who may not be the best guy.

Sydney needs to outsmart Sark in order to retrieve important information. Also, Jack faces Irina after 20 years. And Will meets Vaughn, and Sloane is haunted by his wife's death.

After Sydney’s meeting with her mother, Jack becomes worried, and takes drastic measures to ensure her safety. Also, Will meets a mysterious woman.

Sydney discovers a frightening secret while on a mission to follow new age weapons. Meanwhile, Vaughn suspects that Jack is setting Irina up to fail. Also, Sloane tells Jack the truth about Emily's death

Sydney starts to lose trust for her father. Meanwhile, Vaughn and Sydney may have beeen exposed to a deadly virus in Taipei. Also, Vaughn hires Will to help research for a case.

Sydney finds a cure for Vaughn, but to get it, she must make a deal with Sark, that may risk Sloane's life. Meanwhile, Will finds strange inconsistances in 20-year-old IQ tests

Sydney, Jack, and Irina must go to India to stop six nuclear weapons from being released. Meanwhile, Sloane finds out that his wife is alive. Also, Sark joins SD-6.

During their mission in India searching for six nuclear weapons, Jack and Sydney realize where Irina’s loyalty lay. Also, Sloane tells the Alliance that Emily was still alive.

Jack meets Ariana Kane, head of Alliance counterintelligence, who is investigating Emily's abduction and who is blackmailing Sloane. Meanwhile, Marshall has his first mission, with Sydney. Also, Vaughn schedules a CIA pyshc test and Francie becomes suspicious of Will and Sydney's behavior.

Marshall's life is put on the line, after his mission with Sydney. Meanwhile, Jack becomes the main suspect of Emily's disappearance. Also, Vaughn finds out about Jack's murder of Haladki, and CIA agent, and Syndey reveals to Francie that she has a crush on a co-worker.

Ariana Kane questions Sydney about her father's whereabouts. Meanwhile, Jack gets help from Irina for Sloane's blackmailer. Also, while in France, Sydney and Vaughn go out for dinner afterwards, almost exposing their identities to SD-6.

A new director joins SD-6, after Sloane disappears, and confronts Jack and Sydney. Vaughn and Sydney finally shut down SD-6. Also, romance starts between Will and Francie.

Jack, Sydney, and Vaughn are tasked to see whether CIA agent Lennox is a double agent, after one of his missions is compromised.

Sydney makes a decision about her job in the CIA which does not go over to well with Vaughn. Sloane continues his search for Rambaldi artifacts by kidnapping a scientist and putting him under torture. Dixon decides to tell the truth about his job to his wife, who does not take the news too well.

Sloane learns the secrets to a Rambaldi device. Meanwhile, Vaughn begs for the assistannce of Dixon in a mission to rescue Sydney. Will is questioned, and Sydney begins to sense Francie hiding something.

Sydney begins to wonder if Vaughn is loyal to the CIA when she learns that he is being investigated by the Agency. Irina tries to catch Sloane by using a Rambaldi manuscript as bait. Also, Dixon makes a decision.

Sydney confronts her mother, and Emily has to make a decision about her husband.

Sydney tries to save a captured scientist, Neil Caplan, against the wishes of her father. Also, Sloane seeks revenge for the death of his wife. Also, Francie tries to get CIA information out of Will.

A Rambaldi artifact predicts an event will soon take place. Vaughn and Dr. Barnett begin to worry about Dixon after the death of his wife. Also, Sloane recieves information from a monk in Nepal, that changes his life.

Sydney begins to question Will's real identity after he is suspected of being a double agent. Meanwhile, Sark and Irina try to retrieve the Rambaldi heart, and Jack and Sloane make a deal.

Sydney faces off with her mother, and finally learns Irina's true intentions. Meanwhile, Sloane begins his plane, and Will and Sydney learn who the double agent is.