Synopsis - Season Three
For Sydney, it's two years worth of amnesia. Things have changed. Dixon is now head of their CIA group, Marshall and Carrie are having a baby, and Vaughn has left the CIA and is married. So the first day back at work for Syd is a little odd. The other news is that Sloane has a pardon, is a consultant for the CIA, and is head of Omnifam, a world health organization. Syd's skeptical. So's Jack.
Jack's been in solitary for a year for working with Irina re Syd's "murder". Syd makes a bargain with the NSC for Dad's release. Jack reveals he knew Syd was alive - just before his arrest, he found a vid of Syd killing a Russian diplomat. The new bad group is called "The Covenant", motives unknown. The NSC assigns a new liaison to help the CIA with this group, and it's Vaughn's wife, Lauren Reed.
Vaughn returns to the CIA, so he gets to work with wife Lauren and ex-squeeze Syd, which means lost of angst. The NSC assigns Lauren to find the killer of the Russian diplomat Lazarey, whom Syd killed in the vid. And it turns out that Lazarey is Sark's dad.
Sydney gets a clue to her missing two years - she's called "Julia Thorne" by a freelancer. Vaughn overhears but Dixon orders him not to tell Lauren, because the NSC would lock Syd up Sark springs a Covenant big-wig named Bomani from jail. Sloane's pardon was based on turning in Bomani to authorities, so Sloane's in trouble
Sloane avoids dismemberment by Bomani by promising him help, and then goes to the CIA and says he'll be a double agent for them, with Syd as his handler Another surprise - Allison is alive, saved by the Covenant and a Rambaldi medicine. And she gives another clue - the Covenant needs Sydney alive because they want something in Syd's memory.
Sloane gives Sydney a note supposedly from Syd herself, sent to him shortly before she reappeared in Hong Kong, with a code and a key, leading Syd to an address in Rome: Julia Thorne's apartment Not happy with Dixon, Lindsay takes over the JTF. Lauren gets the info that Syd is Lazarey's killer from Sark and tells Lindsay, to Vaughn's dismay.
The NSC arrests Syd in Rome, and threatens her with invasive brain surgery unless she deciphers another code they found in the Rome apartment. Jack, Vaughn, and Sloane help Sydney to escape. Also helping is Lauren, who didn't realize Lindsay was going to torture Sydney.
Once free, Syd and Jack go to the coordinates which were in the deciphered Rome code that Lindsay wanted. They find a box buried in the desert, containing a severed hand with a Rambaldi symbol Syd goes to see a doc recommended by Sloane to get her memories back. He gives her drugs and she starts to remember in a drugged dream state
In the dream, Syd sees herself cutting a cake, labeled "St. Aidan", but the cake turns into Lazarey's hand Then she tries to get to Door 47, but is stopped by herself. She learns that the Covenant kidnapped her, but losing her memories was her own idea
Opening Door 47 in her dream, Syd finds Will Tippen. So now Syd goes real world searching for Will, who is living a new life in the Witness Protection Program. Will is shocked to see Syd alive. Will says St. Aidan was the name of a contact he had in the CIA. He arranges a meeting, and it turns out St. Aidan is Lazarey, alive but minus a hand
Lazarey asks if "they" found "it" in Graz, just before he's kidnapped, leading Syd and Will to a Rambaldi Cube, with a vial containing living tissue. At the CIA, Jack and Vaughn try to make Syd's jail break seem like a Covenant deal to get and trade Syd for a Rambaldi machine the CIA has. Lindsay's not buying it, so he arrests them, and Dixon too.
Lindsay demands Sloane arrange for an assassin to kill Syd at the place for the exchange, or he'll tell all he knows about Sloane. But it's Lindsay who's killed. And so Jack, Vaughn, and Dixon return to the JTF The Cube is stolen from the CIA, and Syd is kidnapped. When she wakes, she finds herelf with Kendall, who knows the whole story about those 2 years
Seems that Kendall learned the story from Syd herself. Syd was kidnapped by the Covenant the night of the Allison fight. They substituted a fake body they with planted with her own DNA. For six months Syd was brainwashed into believing she was a hired killer named Julia Thorne
But that Project Christmas training from Jack made the brain washing ineffective. So Syd plays along, but calls Kendall at the first possible moment, some nine months after her death Kendall needs Syd to work as a double with the Covenant, but Syd wants to go home. When she sees Vaughn with his new girlfriend, she agrees to being Kendall's new agent
While on Covenant work, Syd meets Lazarey, whom she was given orders to kill. The two of them spend months looking for Rambaldi's Cube, which they discover in a cave in Namibia Syd also finds out that the Covenant wants the Cube to fertilizer eggs they extracted from her, for a Rambaldi "second coming". So Syd decides to hide the Cube and erase her own memories
Kendall said nothing till the Cube was stolen, then decided Syd needed to know. Seems that Dixon was also in the know but sworn to secrecy, and apologizes to Syd for not saying anything The CIA discovers where the Cube is, and Syd et al go to the lab, and destroy Syd's eggs and the Cube
They also rescue Lazarey. On the way home Lazarey asks Sydney about "the passenger". Before he can say more, he is shot And surprise - Lauren Reed Vaughn is revealed as the assassin

 

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