After surviving the accident, Sydney escapes from men posing as EMT but they take Vaughn captive. She learns that Vaughn is under investigation as a double agent, and the accident may have been a cover to extract him.
Sydney teams with Renee, a fugitive wanted by the CIA, to track down a killer of a loved one. Meanwhile, Weiss ponders a promotion that would force him to leave his collegues and Jack enlist s a new agent.
Sydney is reluctantly teamed with the new agent, Thomas Grace. In their pursuit of Howard Dean who just stole a deadly substance from a medical lab, they investigate Rachel Gibson, a young spy working for Dean who they accuse of terrorist activities.
Sloane awaits the outcome of his sentencing. Sydney and Rachel travel to Monte Carlo to follow the money that will lead them to Vaughn's killer, Gordon Dean, but when he discovers that Rachel (Mockingbird) is alive, both women are endangered.
Mercenaries attack Sydney and Tom as they try to get their hands on a cryogenic container Renee stole. Meanwhile, Sloan tries to get back with the APO to search for a cure for Nadia.
Rachel is assigned her first solo mission in order to get to stop a man from designing a dangerous weapon before Gordon Dean gets to him. Sydney must guide the neophyte from a distance forcing Rachel to face Kelly, her former friend from the Shed, all by herself. Meanwhile Sloane, under the control of Howard Dean, tries to balance his duties to APO without losing complete control to Dean.
Sydney and Renee steal Dean's package, even though they face competition in the task. Dean calls Sloane in search of his keycard. Sloane confesses to have been in league with Dean in the hopes that Nadia could be cured, but since that was removed as a carrot, he's back with Jack and Sydney. The keycard grants access to a communications hub. Sloane forces a cyanide pill on Dean on the say-so of Ehrmann who claims that Nadia can be cured.
In an effort to retrieve a micropulse bomb, Rachel goes undercover in Brazil. Unbeknownst to her, Sark, who is also undercover, is after the same information.
When Peyton steals a server with Vaughn's CIA file in it, APO tries to track the information down. Sydney is sent to consult with Renie where they are ambushed and Sydney is kidnapped.
Jack calls on former Agent Weiss and the APO team to search for Sydney after receiving a distress call from her. But Jack believes that a larger conspiracy may be in play, thwarting their attempts to rescue her.
Irina Derevko is a surprise partner to Jack and a very pregnant Sydney on a mission to retrieve "The Horizon" - but her allegiances still remain in question -- and Sloane is forced to scramble when Devlin suspects a mole is working inside APO.
Sydney must cut her maternity leave short to rescue her old friend Will from the clutches of Anna Espinosa. What she doesn't realize is that Anna was hired by Prophet 5 and targeted Will specifically to draw out Sydney to get a DNA sample. The DNA is then used to turn Anna into a clone of Sydney using old Rambaldi techniques.
Sloane finds out that Prophet Five's cure for Nadia could kill her. The search for Anna Espinosa continues. Sydney offers Renee a job at APO.
Ghostly visions and conversations with Nadia haunt Sloane while working for Prophet Five. Sydney goes to Vaughn, who is still recovering, with a chip that was found implanted in Rene that has his real name on it.
Sydney partners with Sark, and must stay undercover as Anna Espinoza, to try and uncover Rambaldi's final clue before Prophet Five does. Vaughn sees Isabelle, his daughter, for the first time. Rachel discovers Tom's secret.
Part one of the Series Finale. Pictures of all twelve members of Prophet Five are accquired. Thomas visits Rachel in the middle of the night and they kiss.
Part two of the Series Finale. Vaughn finds Sydney unconscious at the bottom of the ice cave. He revives her, then heand Sydney devise a plan to locate Sloan and his team.