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.

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 Noah 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.

Sydney finds herself face-to-face with her long-lost mother, Irina Derevko, whose intentions for her daughter are made chillingly clear. However, Sydney manages to escape and rejoin Jack and Will in their escape from Taiwan. After arriving back in Los Angeles, Sydney continues her search for Vaughn, not knowing if he is dead or alive after being swept away by a wall of water in Taipei. Will's life is forever changed when he learns the truth about SD-6 and Sydney's life as a double agent. Also, Dixon must decide whether or not to inform Sloane of Sydney's suspicious activities. But Jack intervenes and covers for Sydney who later finds Vaughn who helps her try to track down her mother Irina who's searching for a Rimbaldi artifact called 'the Bible.'

Sydney must travel to Sri Lanka to outwit Sark in order to find a crucial piece of Intel from a computer disk that she recovers from Rabal. Meanwhile, Jack faces Sydney's mother for the first time in almost 20 years in her prison cell to discuss Sydney's well being. Also, Will finally meets Vaughn, and Sloane is haunted by his wife's death when someone begins sending him anonymous letters which have Emily's handwriting on them.

Past demons revisit all the characters as Sloane becomes confused and desperate over clues that his wife may not be dead. At the same time, Will meets a woman who claims to know the truth about SD-6. And Jack tries to convince Sydney that Irina is setting the stage to betray them and will go to any lengths to prove it.

As Dixon struggles with the death of his wife, He refuses to take time off from work until Sloane is brought to justice. But Sydney worries that Dixon's repressed rage could cause more harm that anything Sloane could do.

Sydney and Vaughn are sent to retrieve the Doleac Agenda to gain an advantage over The Covenant. For this, Sydney and Weiss must convince rogue security systems designer Toni Cummings to help the CIA break into a Lethal Response System. Meanwhile, Sark approaches an unlikely ally, that of Lauren Reed, to kill the Covenant's six cell leaders in order to take control of Covenant for themselves.

While trying to retrieve a bomb, Sydney and Vaughn are ambushed by unidentified assailants. Meanwhile, Lauren and Sark continue to solidify their new partnership as the new leaders of the Covenant. Sloane divulges a dark secret to CIA therapist Dr. Judy Barnett about his past involving Sydney and Irina Derevko. Also, Marshall shows the strains of new fatherhood.

Sydney and Vaughn must convince bomb maker Daniel Ryan that they are part of The Covenant in order to find out where he has hidden one of his devices. But Sydney discovers that her ties to the bomber could lead him on a suicide mission when she learns that Ryan's brother was the murder victim that she killed during her interment with the Covenant, and now Ryan wants revenge.

Sydney attempts to rescue Dixon's kids after they are kidnapped by Sark. Meanwhile, Lauren's status as a double agent for the CIA and the Covenant is put to the test when she learns that she has to work with her father; a wealthy U.S. Senator. When Laura's position is compromised, she and Sark decide to frame Sloane for being the CIA mole.

After finding out that Lauren really is working for the Covenant, Vaughn is told by Jack and Sydney to keep up the facade of a happy marriage in order to keep tabs on his wife's activities. But he's in for a shock when he uncovers the truth about Lauren's mother, Olivia, whom is in league with her daughter over the Covenant's activities. Meanwhile, Jack refuses to help exonerate Sloane of his crimes and put in motion a stay of execution, and a monk discloses the identity of the Rambaldi "Passenger" to Sydney.