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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.
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.
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.
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.
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.
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.
When Irina appears at Sydney's house, she persuades Jack and Sydney to go with her to Vancouver to retrieve The Horizon. which is being safely secured in a bank. While they try to get the item Peyton also tries to get it and all the action brings on Sydney's labor.
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 teams up with Vaughn after being kidnapped and being placed in a hypnotic state. What Sydney doesn't know is that the kidnapper is a very familiar face with an obscure interest in her unborn child.
Rachel is called on a mission when a Micropulse bomb explodes on a train. APO believes this explosion can lead to information about Prophet Five. Rachel is asked to go to Brazil and bug Basarov's computer but she runs into Sark in the process who seems to be doing exactly as she is.
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 his daughter Nadia, continues to play mind games with him, Sloane struggles for control.
Rachel goes on her first mission while her family is placed in the witness protection program for their safety. Meanwhile APO sets up a trap using János Vak as bait which they hope will capture Dean, and they set Rachel the task of bringing him in.
Syd and Tom discover that Renée has stolen the cryo container, and soon find themselves under siege by a group of mercenaries who want the contents of the container. Meanwhile, Sloane takes matters into his own hands to get himself back into APO and continues his quest to find a cure for Nadia.
When Gordon Dean discovers Rachel is still alive he captures Sydney while she is returning from a mission. He demands that Rachel should be returned to him but Sydney is reluctant to agree to his terms. However, if Sydney refuses she could face almost certain death. Meanwhile Sloane goes before a judge.
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. Meanwhile, Dixon must accompany Sloane, who's given a 48-hour pass from prison to acquire a possible cure for his daughter, Nadia.
Sydney teams up with Renée - a fugitive on the CIA's most wanted list -- to track down Vaughn's murderer 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 friends and colleagues.
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. When she discovers that she's pregnant with Vaughn's baby, she becomes determined to uncover the truth about him. Meanwhile, because of Jack's past betrayal by Irina, he begins to worry that his daughter may suffer the same fate that he did.
