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.
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.
Sydney gives birth to the baby, but Sloane may need something from the newborn. Nadia awakens.
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. What Sydney doesn't know is that the kidnapper is a very familiar face with an obscure interest in her unborn child.
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 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 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 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.