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Alias Series Summary - Season Three

Picking up where the previous season ended, Vaughn has met Sydney in a Hong Kong safehouse; he tells her that there was a fire in her apartment the night she fought Francie's double. Will survived the fire, but remains found there matched Syd's DNA, so they thought she was dead. After Sydney's "death," Vaughn left the CIA to become a teacher. However, the Agency asked him to come, thinking it best if a familiar face "reintroduced" her to everything. In disbelief, Syd attacks Vaughn - thinking him a fake - and flees, but he shoots her with a tranquilizer dart.

She wakes in a naval hospital: Dixon is there. He tells her that it was Vaughn who met her in Hong Kong, and that Vaughn told her the truth. Dixon is now the head of their division at the CIA. Weiss arrives to speak to Dixon, and though they step out of the room, Sydney watches them through the glass in the door. When Dixon returns, he reveals that Jack has been imprisoned by the National Security Council (NSC), and he is not allowed to have visitors. Later, as Weiss sits with Syd at the hospital, she declares that she thinks she remembers where she was.

Syd returns to the CIA and observes that there are many new faces. She is thrilled to see Marshall, and to learn that Carrie is pregnant - with Marshall's child. Marshall says that they're not married *yet* but Carrie insists that they're not even engaged. They later get married - in a very informal ceremony - not long before Carrie gives birth to their son, Mitchell.

Syd is introduced to Robert Lindsey, the NSC liaison. Dixon questions the memories that Syd seems to have, and the group believes that she was held by a powerful new terrorist group called The Covenant. The Covenant's latest attack earned them a valuable computer chip, and Dixon shows Syd a picture of one of The Covenant's outposts, asking if the place looks familiar. Sydney says that it does, and Lindsey wants her to go on the mission with the team to retrieve the chip. Sydney says that she will go, but only if she can see her father.

Lindsey agrees, and Syd visits Jack in prison. Jack explains that he became obsessed with finding those responsible for her death, so he worked with the one person he knew he could trust: Irina. Since Irina was number six on the CIA's most wanted list, when Lindsey found out, he had Jack thrown in prison to make an example of him. Using an anti-eavesdrop device she obtained from Marshall, Syd confesses that she doesn't remember anything: she had been reading lips during Dixon's conversation and she saw an opportunity to bargain to get to see Jack. Jack encourages her to continue with the mission and regain her clearance.

On the mission, the team is ambushed, but Syd saves Weiss. She confesses that she lied about remembering, but she declares that she will find the chip and use it to free her father. Weiss encourages her to go see Sloane, who now runs a World Health Organization in Zurich called OMNIFAM, as well as being a consultant for the CIA.

Syd visits Sloane, but she still doesn't trust him. He speaks of redemption, saying that the Rambaldi device after it was assembled revealed one word: peace. That resulted in Sloane having an epiphany and changing his evil ways; he started by providing info that the CIA used to dismantle several terrorist cells. Sydney says that she knows him too well and doesn't believe it.

Sloane helps Syd identify one of The Covenant's men that she saw during the raid, which in turn helps her track down the chip. She marches into Lindsey's office, threatening to destroy the chip if her father isn't released. Lindsey reluctantly agrees.

Syd sees Vaughn at the CIA building. He says that he came to see how she is, but she is furious at him for giving up hope after all the madness they've seen. She says that she wouldn't have given up if the situation was reversed, but she adds coldly that now she sees what a waste that would have been.

Jack returns to work at the CIA, and takes Syd aside. While she was missing, he found evidence that she was alive: video footage in which a blonde Syd greets Andrian Lazarey, a Russian diplomat, but slits his throat when the man turns his back. Seeing that, Syd says that she doesn't trust herself, but Jack advises her not to tell the CIA about the murder.

Vaughn returns to work at the CIA. He tells Syd that he loved her so much that losing her almost destroyed him, but he doesn't regret moving on with his life.

The Covenant's next move is to kidnap two CIA agents. One is murdered and The Covenant wants to trade the other for Sark, who is still imprisoned by the CIA. Lindsey agrees to the exchange, but thanks to his attempt to attack The Covenant, they escape with both Sark and the hostage. Later, Jack discovers that The Covenant used Sark to withdraw $800 million in gold bullion from a bank; the gold belonged to Lazarey and after his death, it went to his son: Sark. Following a lead, Syd finds the missing CIA agent and shoots the man who was torturing him. As the torturer dies, he remembers that Syd had vowed to kill him, adding that she was his favorite because she never broke.

Lindsey leaves for Washington and Syd meets the new NSC contact, Lauren Reed - who is also Vaughn's wife. Jack soon learns that Lauren has been put in charge of investigating Lazarey's murder.

Sydney finds another mysterious clue to her past when a mission to thwart a Covenant plan puts her in touch with the mercenary Simon Walker; to her surprise, Simon recognizes her as Julia Thorne and kisses her passionately. Sydney continues with her plan to join his crew, but unfortunately Simon's men catch Vaughn in the CIA van. Simon is going to shoot Vaughn, but Syd plays the part of betrayed Julia and stabs Vaughn. As soon as possible, she calls Jack, who sends a team to locate Vaughn. Syd returns to LA and finds Vaughn in serious condition in the hospital, but Sydney insists on confessing to Lauren that she was the one who stabbed Vaughn.

Not much later, as the two travel to Zurich to question Sloane, Lauren threatens to have Sydney transferred. Before the women can get to Sloane, he is taken captive by Sark and Bomani, a powerful arms dealer that The Covenant freed from prison. Not much later, Sloane is released, and he confesses that The Covenant wants him to work with them. He proposes that he act as a double agent and report on The Covenant's activities to the CIA. Sydney is very skeptical but Marshall's lie-detector tests seem to verify Sloane's sincerity. Lauren says that the NSC proposes they accept Sloane's offer of becoming a double agent. Dixon assigns Sydney to be Sloane's handler.

After hearing Simon call Sydney Julia, Vaughn becomes suspicious of Sydney's activities during her missing years. She refuses to tell him anything, and he tries to question Jack with the same result. In a surprise move, Jack shows Dixon the video of Lazarey's murder. Dixon is displeased that Jack and Syd hid it from him, but he wants to keep it from the NSC for the moment. He forbids Vaughn from telling Lauren about it, and Vaughn feels guilty for hiding information that is critical to her investigation.

Sark, working with The Covenant, gets a new partner: Allison Doren, aka "Francie's evil double." He is stunned to learn that she's alive. She explains that she woke up three weeks after the fight with Sydney, in a hospital that was run by The Covenant. It took her six months to fully recover, and she started working with them.

The CIA is also aware that Allison is alive. Dixon shares that news with Sydney, and the two women soon cross paths as they hunt the same target. Allison knocks Syd out, but leaves her unharmed; Syd wonders why, and Allison says later in a meeting with Sloane and Sark that The Covenant wants to retrieve something from Sydney's memory. Not much later, Syd and Allison cross paths again. As they fight, Allison says that the Rambaldi journal that Syd found contain a formula for a medicine that healed her wounds. Syd is able to shoot Allison again, and although severely wounded, she recovers well enough to escape from the ambulance en route to a hospital.

Suffering from nightmares, Syd becomes more desperate to know what happened to her. She questions a CIA psychiatrist about a surgical procedure to recover lost memories, but he warns against it saying that it would likely result in brain damage.

Sloane gives Sydney a letter that he received the day she appeared in Hong Kong: addressed to Sydney in her own handwriting, it contains a key and a piece of paper with numbers on it. Jack discovers that the key is to an apartment in Rome.

Wanting revenge against Sydney for killing his father, Sark approaches Lauren in the CIA garage and gives her pictures from the video footage which prove that Sydney is Lazarey's killer. Lauren is later shocked again to learn that Vaughn and the others have known for weeks. Fearing that Lindsey would subject Sydney to dangerous surgical procedures to discover her memories, Vaughn tries to convince Lauren not to report Sydney, but he realizes that she already did. He helps Sydney flee the country, vowing that he won't lose her twice. She travels to the apartment in Rome where she recognizes a statue from her dreams. Unfortunately, the Italian police catch her by surprise and declare her under arrest by order of the NSC.

Sydney is taken by the NSC for interrogation, and Vaughn and Jack form a plan to extract her. Despite Lindsey's assurance to Lauren that Syd is being treated fairly, she is tortured, but she refuses to crack. However, when Lindsey's men torture a fellow prisoner, Syd quickly confesses that the numbers from her Roman apartment are for coordinates. She then learns that the fellow prisoner was a plant; Sydney's profile revealed that her major weakness is empathy. With the help of Sloane and Lauren, Jack and Vaughn free Sydney from the NSC's custody.

The group decides to frame The Covenant for Sydney's extraction. As they decide what to offer to trade her for, Sloane suggests that the Rambaldi device would be a logical choice. This arouses Syd's suspicions, but Jack declares that when they get the device, they will destroy it. Sydney reveals that she gave Lindsey the wrong location for the coordinates: searching at the correct location, she and Jack find a box containing a severed hand bearing a Rambaldi tattoo.

Lauren returns to Lindsey to tell him of the Covenant's "demand." Lindsey is skeptical but he agrees to the exchange. However, he meets with Sloane, saying that he knows what Sloane's endgame is. Lindsey says that he wants Sloane to make sure that Sydney doesn't live through the exchange.

Meanwhile, Sydney, Jack, and Vaughn visit Dr. Brazzel, who has developed a non-invasive procedure to help those suffering from memory loss. The procedure uses a certain mix of drugs to achieve a dream state from which memories can be accessed. Syd undergoes the therapy; in her dreams she experiences a semi-random string of memories, which includes following the men who abducted her after her fight with Allison. They take her to Room 47, but Lauren guides her away before she can explore further. Later, out of the dream state, Syd tells Jack and Vaughn of her dream that she cut off Lazarey's hand. Syd also reveals that Lauren strangled her in the dream, but Brazzel says it's unclear if it was Lauren, or simply a representation of someone else. Under the therapy a second time, Sydney again finds Lauren who morphs into a double of Sydney. The double seems intent on stopping Syd, but Syd defeats her and hurries into Room 47 where she is shocked to see Will. She also sees a recurring name: St. Aidan. Before she can speak to Will, the others awaken her, fearing for her safety since she had started to flat-line.

The hand that Jack and Syd found proves to be Lazarey's and tests reveal that he was alive as recent as four months ago. So, Sydney did not kill him, and the video of his death was a fake.

Dr. Brazzel believes that Syd's memory of the missing time has been removed and that the precision of the extraction may indicate that she was a willing participant.

Jack advises Syd to contact Will, who has been in the witness protection program. Syd visits Will; thinking her a fake, he pulls a gun on her, but she is able to prove her identity. He reveals that St. Aidan was one of his contacts; he sets up a meeting, and Sydney recognizes the man to be Lazarey. Will mentions Julia, and Lazarey asks if they have found "it" and if "they" have been to Graz. Sark crashes the meeting and escapes with Lazarey. Hiding out in a hotel, Syd and Will catch up on old times, and they wind up sleeping together. The next morning, Syd pieces together where Julia might have hid the object in question: in a hotel's safe deposit box. However, Sark tortures his father - whom he remembers to be physically abusive - and discovers the object's location. He and Allison arrive first. Syd chases down Sark and retrieves the object, a small metal cube. Allison attacks Will, and they fight, but he ultimately stabs her. She slumps to the floor, seemingly dead. Will later reveals that her death didn't really give him closure. He starts to leave, but he vows to Syd that they'll see each other again.

Syd returns home, but during the bogus exchange with The Covenant, the assassin that Sloane hired kills Lindsey instead. The Rambaldi device is also missing; Sloane insists that Lindsey never gave them the device, but Sydney doesn't believe him.

Some time later, Syd is tranquilized at her apartment; she awakes on board a jet, where she is surprised to find Kendall, who confesses that he really works for the Department of Special Research. The cube she found has been stolen by The Covenant during transport. To explain how this affects Sydney, Kendall says that she called him nine months after her funeral, having escaped from The Covenant. She told him everything she had been through: she had been tortured as her captors tried to brainwash her into believing that she was Julia Thorne. She had even killed a prisoner of The Covenant to prove that the brainwashing had been successful. Syd is shocked to learn this, but Kendall explains that her Project Christmas training prevented her from being turned. Kendall said that he encouraged her to return to the Covenant as a double agent, posing as Julia. Syd had wanted to see Vaughn to let him know she was alive, but instead she observed him happy, with Lauren, and Syd knew that to keep him safe she must stay away.

Kendall continues the story by explaining that Syd returned to The Covenant, where she discovered Lazarey who was close to uncovering the artifact. The Covenant wanted her to kill him, but they worked out a deal - they faked his death (in the video that Jack found). Kendall explains that instead of delivering the cube to him as planned, Syd sent him a videotaped message. On the tape, a blonde Sydney explains that since so much has happened to her, she is having an experimental procedure done to erase her memory. She says that she has hidden the cube and with her memory extracted there will be no way to find it; she also asks Kendall to never tell her what she's been through, if she ever comes to him and asks about it. Kendall explains that Rambaldi's followers believe that he will return by way of a child, and The Covenant will use the DNA in the tissue from the cube to fertilize the egg of the Chosen One. Remembering her mysterious scar, Syd realizes in horror that they extracted her eggs. Syd also realizes that she had been tricked into finding the cube.

As Kendall predicted, elsewhere in the world, Sark observes a series of test tube fertilizations. Thanks to Marshall, The CIA locates the cube; Syd, Dixon, Vaughn and Weiss storm The Covenant's facility, where they find the fertilization equipment. Kendall wanted it brought back for analysis but Dixon allows Syd to torch it all. Vaughn and Weiss rescue Lazarey; as Sark flees, he makes a phone call ordering his father to be killed. As Lazarey is transported to a hospital, he asks Syd if she knows about The Passenger. Seconds later, he is shot. On a nearby rooftop, Lauren packs her rifle into a case and calls to report that the matter is taken care of before she hurries away.

Syd and Vaughn try to fight their feelings for each other. Jack urges Vaughn to push Sydney away, but they finally confess when they're imprisoned on a dangerous mission. However, when they return home, Vaughn hurries to embrace Lauren. Later, Syd tells Dr. Barnett that she feels Vaughn is her soulmate.

At Jack's suggestion, Sloane calls Dr. Barnett under the guise of needing help, but he tries to elicit information from her about Jack and Sydney. Dr. Barnett persists in trying to help him, and Sloane finally admits that he had an affair with Irina. Sloane says that he never tried to prove that Sydney was his daughter, but he likes to think that her strength comes from him.

Sark discovers that Lauren works for The Covenant, and he proposes that the work together to gain more power. She agrees. Their power play worked as the man in charge - MacKenas Cole - places them in charge of the North American cell. Along the way, they also begin a torrid affair.

At Dixon's request, Jack begins an investigation to find the person that is leaking information from the office. The source of a mysterious transmission turns out to be from OMNIFAM's IP address, and Sloane is arrested. However, a slip of the tongue clues Jack in to Lauren, and the evidence confirms his suspicions. Jack presents his findings to her father, Senator Reed, who defiantly says that his daughter is a patriot.

Vaughn tells Lauren that he wants to separate. Sark suggests that Lauren murder her father, so that Vaughn will return to her out of compassion, as he did with his former girlfriend, Alice. Lauren at first refuses, but finally she relents. She goes to see her father, who is now sadly convinced of her guilt. He offers to cover for her, and she appears torn over whether to proceed. However, her mother, Olivia comes in and shoots the man herself. They convincingly frame him as the mole, and Vaughn returns to Lauren.

Although Sloane is no longer suspected of being the mole, evidence found in Senator Reed's records show that Sloane provided him with Rambaldi artifacts. Dixon tells Sloane that his pardon has been revoked, and he will be executed in two weeks.

Sydney begins to suspect that Lauren truly is the mole, but Vaughn won't listen. He finally believes when he finds evidence in a hidden panel in her suitcase. Vaughn is furious, but Jack advises him to play along so they can use this knowledge to their advantage.

The CIA learns that The Covenant is searching for the person known as The Passenger. Sydney learns from the Rambaldi monk, Conrad, that The Passenger is her half-sister, the daughter of Irina and Sloane. Syd finds a Rambaldi device that will reveal the location of The Passenger, but only to her father. To this end, Jack fakes Sloane's execution to free him from CIA custody. Sloane explains that there is an elixir that will enable The Passenger to channel a message from Rambaldi; Sloane wants to protect his daughter from The Covenant, who would expose her to large doses of the elixir to obtain the message.

Vaughn learns that his father was a follower of Rambaldi: Bill Vaughn freed The Passenger from KGB custody, but he didn't trust the CIA either, so he hid the girl, and that is why Irina killed him.

Jack, Syd, and Sloane locate The Passenger in a prison in Chechnya, and Syd breaks in to free her. The young woman's name is Nadia Santos, and she fights almost as well as Sydney. Back at the safehouse, she recognizes Sloane, who says that he changed his evil ways for her. However, he causes a diversion and escapes with Nadia, who wakes strapped to a table. Sloane injects her with the elixir, and she begins to write in a trance-like state.

At one point, Nadia gets free and destroys Sloane's supply of the elixir before he knocks her out. Sloane tries to locate more of the formula, but Sark and Lauren arrive with it. At one point, Sloane insists that Nadia needs rest, but Lauren and Sark try to force him to increase the dosage. Before they can do so, the CIA storms the compound. Sloane, Sark, and Lauren escape, but the CIA obtains the Rambaldi message, which is an equation. Nadia tells Sydney that Sloane tried to protect her.

Olivia realizes that Vaughn is on to Lauren. Disguised as Sydney, Lauren sneaks into the CIA offices and obtains the Rambaldi equation; she also shoots Marshall who happened to be in her way. Lauren escapes, but Sark is captured in the parking garage. Vaughn takes off after questioning Sark, and Syd realizes that he is out for revenge against Lauren. Syd calls Vaughn, encouraging him not to do it. Vaughn catches Lauren, but someone stabs him in the back and frees her. With Vaughn in the hospital, Syd vows to Jack that she will kill Lauren herself.

Sloane approaches Nadia for help in finding the object revealed by the equation: the Sphere of Life. At first she doesn't trust him, but she finally admits that as she was coming out of the effects of the fluid, she altered the equation, so that the others are looking in the wrong place.

Syd finds Lauren at the site where The Covenant is (wrongly) digging. They fight, and Lauren taunts Syd that she still doesn't know the truth about her life. Lauren gets the upper hand, but Vaughn appears, having come to warn Syd that it was a trap. He shoots Lauren several times and she falls down a mineshaft.

Using clues that Lauren gave her, Sydney locates a certain bank box. In it, she finds top secret papers that tell of an "active project" that started on her birth date - with project manager Jack Bristow. Syd cries as she reads the documents. Jack suddenly appears, telling her she was never supposed to have found them.

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