Sydney Bristow discovers that her job as an agent for SD-6, a top-secret division of the CIA, is not what she thought it was. Sydney's father, Jack, also tells her the truth about his work and she, enraged, seeks help from real CIA and is hired as their double agent under the command of Agent Vaughn. From now on, her job is really simple: she needs to complete her cases at SD-6 while reporting her findings back to the CIA.

Sydney is heavily questioned by the FBI concerning her past and her current activities at SD-6. Fearing that the FBI might detain her longer, Jack and Vaughn must find a way to make her escape before she blows her cover with SD-6...

When a young CIA agent dies, suspicion immediately falls on her parter and lover, agent Jim Lennox. But after Sydney rescues Lennox from captivity, She trikes up an instant connection as they discover shared wounds - realizing They've both lost someone they love to the job. Yet even her judgment is thrown when Vaughn and Jack discover that Lennox was pursing a technology that allows people to change their appearance. Now Sydney must ask herself: is this the real Jim Lennox - or is his double?

Sloane decides to betray Dean when he learns that Nadia's condition will probably not improve. They meet at a race track in Dubai to exchange a network access card which Sydney and Renee stole in Rome, leading to Dean finally being captured. The APO interrogates Dean for information on Prophet Five. Yet another mysterious stranger asks Sloane to eliminate Dean. Meanwhile, Nadia comes out of her coma for a short time after a nameless nurse leaves her room. Under orders from his new Prophet Five contacts, Sloane kills Dean during a routine reboot of the APO's surveillance network, and APO misses its chance to hack the network, but learns Prophet Five is linked to intelligence agencies around the world. At the end, control of Dean's terrorist cell is given to Kelly Peyton.