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...

After turning herself in to the CIA, Irina won't communicate with anyone - except her daughter. Sydney refuses to cooperate, until a mission goes awry and crucial information falls into the wrong hands. Now, against Jack's wishes, Sydney must face Irina and find out what She knows.

Sydney must travel to Sri Lanka to outwit Sark in order to find a crucial piece of Intel from a computer disk that she recovers from Rabal. Meanwhile, Jack faces Sydney's mother for the first time in almost 20 years in her prison cell to discuss Sydney's well being. Also, Will finally meets Vaughn, and Sloane is haunted by his wife's death when someone begins sending him anonymous letters which have Emily's handwriting on them.

Past demons revisit all the characters as Sloane becomes confused and desperate over clues that his wife may not be dead. At the same time, Will meets a woman who claims to know the truth about SD-6. And Jack tries to convince Sydney that Irina is setting the stage to betray them and will go to any lengths to prove it.

As Vaughn's life hangs in the balance, Sydney has no choice but to turn to Sark for help in securing an antidote for the virus. But when Sark demands She help him to kill Arvin Sloane in exchange for his assistance, Sydney faces a decision that could expose her as a double agent.

Sark's alliance with SD-6 suddenly puts Sydney at risk of being exposed as a double agent. She has no choice but to cooperate with his plan, until his alliance with Sloane sends several nuclear weapons into the wrong hands. Now, only Irina holds the key to unraveling Sark's agenda - and She refuses to cooperate.

Still trapped in hostile territory in Pakistan, Sydney, Jack, and Irina continue their search for the missing nuclear warheads held by PRF's leader Gerard Cuvee. After several misadventures, they arrive at Cuvee's stronghold, only to be betrayed by Irina. Back in the USA, Vaughn wants to mount a secret rescue mission to Pakistan before Kendell authorized the Indian army to launch an air strike on the facility with Jack and Sydney held captive inside. Meanwhile, Sloan decides to pay off his unknown blackmailer.

When Sydney learns that Marshall has been kidnapped, she struggles against a heartless Sloane to bring Marshall back whom is being tortured by the same Taiwanese torturer Dr. Lee "Suit and Glasses" to uncover the code for the top secret ECHELON security system whom tries to stall for time. Sydney and Dixon are instead sent to Ho Chi Minh City, Vietnam to recover the hard drive for ECHELON. Meanwhile, Kendall and the rest of the CIA frantically tries to prevent SD-6 from gaining access to ECHELON... and Jack realizes that the only one who can help them is Irina.

Sydney and Vaughn reach a crossroads as they try to turn a professional relationship into a personal one during a mission to recover an experimental gyroscope. Meanwhile, Jack struggles to outwit the persistent SD-6 security expert, Ariana Kane, as she tightens the noose of suspicion around him of being Sloan's blackmailer.

The entire world of 'ALIAS' is turned upside down. Sloane disappears mysteriously and Anthony Geiger becomes the new head of SD-6. As the Bristows struggle to keep their secrets safe and stay one step ahead of Geiger, Will and Francie make a startling discovery of their own while Francie prepares to open her new restaurant. After an airborne mission, Sydney uncovers crucial information that could shut down SD-6 and bring down the entire Alliance.

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?

Sydney finally has the opportunity to leave the CIA for good, but a startling phone call from Sloane, combined with the kidnapping of a brilliant mathematician, brings her back into the fray.

When Sloane gets his hands on a terrifying Rimbaldi weapon that causes internal spontaneous combustion, Sydney must turn to a betrayed and hurt Dixon for help. But when her ex-partner refuses any assistance, She has no choice but to carry out the mission herself. When Sydney is captured, Vaughn must persuade Dixon to help the CIA rescue Sydney from an Afghan warlord's camp.

When Sydney learns that Vaughn is under investigation for being a double agent, Jack and Irina forge an unlikely partnership in their attempt to get their daughter out of the CIA for good. Kendall learns that Sark and Sloane are attempting to get their hands on a Rambaldi manuscript detailing the works of the human heart, so he sends Jack and Irina to Bangkok to learn more, and then to Panama to capture Sloane. But Irina betrays Jack and escapes from custody... this time for real.

Following her betrayal, the CIA try desperately to track down Irina Derevko. Their trail on Derevko leads them to Stuttgart and closer to Sark and Sloane, even as Sloane contemplates giving up his quest to complete Rambaldi's work in order to stay with his wife, Emily.

Sydney finds herself racing to clear Will's name when the Francie impostor frames him for the CIA intelligent leak by making him appear to be the other double of the Helix project. But Sark makes matters worse when he sends a team to extract Will, to make it look that he's guilty. Meanwhile across the globe, Irina and Sark discover a stumbling block could turn into an opportunity... with Sydney's cooperation.

Sydney must confront her mother, who tells a clue about "some Rambaldi artifacts" in Zurich, but it was a trap to capture Jack. As Sloane keeps Jack hostage, Vaughn and Sydney go to Stockholm to capture Sark, who reveals the hideout in Mexico City. Meanwhile, Tippin discovers that Francie is in fact a "double" and is the one who framed him...

In this episode, Sydney finally learns the shocking truth about her missing two years from an unlikely source: FBI Special Officer Kendall. Kendall whisks her away and talks to her from the privacy of an airborne 757 jet. According to Kendall, Sydney was captured by the Covenant after her fight with Francie/Allison, held captive in Russia for over a year and brainwashed to become an assassin. But Sydney only pretended to be brainwashed and contacted Kendall who became her contact and handler, thus giving him information about the Covenant and about their quest for Rambaldi artifacts. Sydney also staged the murder of Andrian Lazarey, and then deliberately had her memory erased to prevent the Covenant from knowing about secrets she had learned about Rambaldi's findings.