Sydney Bristow, an agent who has been tricked to believe she is working for the U.S. government, is actually working for a criminal organization named the Alliance of Twelve. Upon learning this, Sydney becomes a double agent for the real CIA.
After learning that the man she has known as Michael Vaughn is under investigation and suspected of being a double agent, Sydney begins to question whether their business and personal relationship over the years had all been a lie.
Sydney teams up with Renée - a fugitive on the CIA's most wanted list -- to track down the murderer of a close friend before the killer can strike again. Meanwhile, Jack enlists a reluctant new agent, Thomas Grace (Balthazar Getty), and Weiss struggles to decide whether or not to accept a promotion that would force him to leave his colleagues.
Sydney is forced to partner on a mission with new APO agent Thomas Grace. They discover that Rachel Gibson -- a spy suspected of being involved in activities against the U.S. -- has something shockingly in common with Sydney.
While Sloane awaits the outcome of his sentencing, Sydney's life is put in grave danger when Gordon Dean discovers that Rachel is still alive.
Sydney and Tom discover that Renie has stolen the cryo container, and soon find themselves under siege by a group of mercanaries who want the contents of the container. Meanwhile, Sloane takes matters into his own hands to get himself back into APO.
Rachel receives a little help from Syd for her first solo mission while Sloan is back at APO in frequent contact with Gordon Dean.
Sydney and APO attempt to discover whom Gordon Dean is working for and what their end game is. Meanwhile, when the group claiming to have a cure for daughter Nadia continues to play mind games with him, Sloane struggles for control.
Rachel and Sydney have to join forces with Julian Sark to prevent a deadly micropulse bomb from falling in the hands of a dangerous mercenary.
Sydney teams up with Vaughn after being kidnapped and being placed in a hypnotic. What Sydney doesn't know is that the kidnapper is a very familiar face with an obscure interest in her unborn child.
The entire APO gang is trapped inside the CIA offices and Weiss saves them. However, Weiss will not be returning to APO, he will just be helping the others on a mission to obtain information regarding Sydney.
Sydney gives birth to the baby, but Sloane may need something from the newborn. Nadia awakens.
One month after the baby is born, Sydney is taking time off from work. Will is what pulls her back in the field while she's on maternity leave. The enemies realize that the best way to hurt Sydney is through her friends. Anna Espinosa also returns.
While the gang starts to learn more about the Prophet 5, Sloane is distressed to learn that Prophet Five's cure for Nadia is just as likely to kill her. Meanwhile, Devlin returns, the search for Anna Espinosa continues, Rambaldi's prophetic Page 47 resurfaces, and Sydney offers Renée a job at APO.
Marshall reports to Jack that a microchip, found in Renée Rienne's body, is etched with the name 'Andre Micheaux'. Peyton tells Sloane that Sydney is being sent to Nepal to meet with someone regarding the chip. Sloane sends Anna, now Sydney's doppelgänger, to intercept. When Marshall discovers that the APO office is bugged, Jack frantically tries to reach Sydney to warn her before it is too late.
Sydney now posing as Anna, brings Peyton a microchip with a device hidden in it. Meanwhile Sloane finishes translating page 47 and reports that only the chosen one can complete the circle, which leads Sark and Sydney on a dangerous mission to a prison. Rachel finally discovers Tom's secret about what happened to his wife.
In the first part of [the] Alias two-hour finale event, 'Reprisal,' Sloane takes Marshall and Rachel hostage in order to discover a crucial clue to Rambaldi's ultimate endgame, as Sydney, Vaughn and APO race to stop him.
Peyton tells Sloane that she has made a deal for the Rambaldi Sphere with an ally in China. Sloane arranges for stolen missiles to be sent to Hong Kong. Sloane's plan is revealed to the APO members, who race to stop him before he can use the Rambaldi Sphere to put the plan in motion. But this all leads to a long awaited confrontation between Sydney and Irina.