Alias

Sydney and Vaughn are in the car, on the way to Santa Barbara, and as in the previous season finale, he tells him that his name is not Vaughn, just before they get hit by a car coming from the left.
Right after that, we see the accident location, with only their car, on the side of the road, close to a cornfield. Sydney wakes up and sees Vaughn who has passed out. She passes out herself and when she opens her eyes again, a rescue team is on the location and one of the rescue members tells her that they will rescue them soon, while he prepares her an injection.
She smells a rat when she hears one of the rescue team sending a radio message mentioning that she was alive. As the medic approaches to give her the shot, she manages to make him get the shot himself and as he collapses, she escapes into the cornfield. She is chased by two men that she eventually kills. She then sees the "rescue team" put Vaughn, who is lying on a stretcher, in a helicopter. Sydney takes a god look at the face of the co-pilot.

At the hospital, the doctor tells Sydney that they have to run some more tests, but other than that, she is fine but should take it easy. While she is putting back her engagement ring, Gordon Dean, from special investigations enters her room and starts questioning her about her and Vaughn, and asks if he was preoccupied, to which she answers that he seemed relaxed. He tries to pressure her by reminding her where her loyalty should lye (her fiancée or national security). He is interrupted by Sydney's father, Jack, who just entered the room and gently asks him to stop his interrogation, mentioning that Sydney will cooperate, but when she has recovered. Once alone with Sydney, Jack reminds her of the risk of being kept prisoner by the CIA, as they suspect that Vaughn could be a double agent and that the car crash could have been an extraction.

Unknown location: A man enters an interrogation room in which Vaughn, still covered by his blood from the crash, is sitting. The man says that he is pleased to finally meet Vaughn and calls him Mr Michaux

In the subway, on her way to APO, Sydney sketches the face of the helicopter co-pilot. Once there, she sees Jack talking to Dean.

Back to Vaughn: He has a dislocated shoulder. The man lets him believe that they have Sydney in detention and hands over to him an envelope containing a tape recorder. Vaughn faints not knowing what to do with it, but his interlocutor opens one of the batteries in which lies a paper containing an encrypted message. As Vaughn refuses to say where a certain Lehman is, one of the guards tortures him on his bad shoulder.

APO: Sydney asks Weiss why Vaughn was assigned to her case. Weiss tells her that he volunteered, as she seemed to be a challenge. He mentions that he does not believe in the idea that Vaughn could be disloyal.

Back to Vaughn: Vaughn's interlocutor threatens to cut one of Sydney's fingers, which makes Vaughn agree to decode the message.

APO: Dean asks to Marshall to hand over Vaughn's file. Marshall says that the operation will take some time. Marcus checks out on Sydney and reminds her of the old time at SD-6, when he caught her as a traitor, but gave her the benefit of the doubt.

Back to Vaughn: Vaughn pretends not to be able to write and asks to have his dislocated shoulder fixed. Once done, he assaults his interlocutor and the guard, who finally admits that Sydney escaped, and escapes.

APO: Sydney gets a call from Vaughn. She goes to the bathroom for some privacy, as we see that Dean is looking at her in a suspicious way. Vaughn's asks her to bring him his father's watch, by depositing it in a locker they both know. She answers that she needs to think about it. As she leaves the bathrooms, Dean and her father await her. Dean reminds her that withholding information makes her guilty. Jack tells her that she needs to give Vaughn location, because he might really be a traitor, and if not, then he might be in danger and bringing him in would be his best protection. She then answers that Vaughn is in Mexico City.

Sydney actually gave the CIA a false location. As they make a useless raid at what seems to be a deserted fabric outside of Mexico City, Vaughn opens the locker to find no watch, but Sydney, holding it. She demands the truth. He presents himself as André Michaux and says that he will say the rest on the way.

Unknown location, in an elevator, to visit Lehman: Vaughn/Michaux says that 7 years earlier, a woman came to him and told him that his father was a mathematician involved in a secret research project called Prophet Five. That happened before he became a CIA-agent and that his name was then Michaux. He explains that the day Sydney walked in the CIA for the first time, her mention of a device designed by a certain Mueller, who was the one who sat up Prophet Five, was the first proof he ever had that the woman who approached him told the truth. At the time, his father was running away from the project and had changed his identity and Vaughn's who was 18 months old. He says that it took years for him and Renée Rienne to locate him. They meet Lehman who demands to see the watch and makes a remark on Sydney's presence.

APO: Dean accuses Jack of protecting Vaughn and Sydney and announces that he will officially declare Vaughn as a fugitive and Sydney as an accomplice. Once Dean is gone, Marshall tells Jack that he gave Dean an encrypted version of Vaughn's file, which will take Dean ages to decode.

At Lehman's: Lehman explains that he was a cryptologist, a specialist in patterns, working with the Pentagon. A private foundation recruited him in 1972 along with other linguists and scientists such as Vaughn/Michaux's father. They were working on one page of a book called Profeta Cinque, fifth prophecy, dating from the 15th century and written in a supposedly unbreakable code. They managed to break the code after years of research and the content of the page referred to a kind of advanced genetics 500 years ahead of its time. Some days after handing over the work to the foundation, Lehman was contacted by Vaughn/Michaux's father who urged him to go underground, as their colleagues in the project were dying one after the other of accidents, fires, heart attacks. He resurfaced now because he had a lead on where the book might be. He warns Vaughn/Michaux that the people after the book will kill if necessary, to shut them up.

Cape Town (first mention of a location): Sydney and Vaughn/Michaux pretend to be a French speaking couple and manage to attend a reception in a house facing a cliff over the sea. Sydney drugs a glass of champagne the owner drinks and he soon collapes on the ground. As everybody converge to him, Vaughn/Michaux goes to the room where the safe lies and Sydney goes to another room where electronic boards are. As the security system for the safe has been customized, she calls Marcus for help with this specific model she wants to break in. Marcus gives her (again) the benefit of the doubts and helps her out. Meanwhile, Vaughn/Michaux gets the visit of the owner's daughter. After some (hot) socializing, she leaves the room, and Vaughn/Michaux can take the book as the safe has got opened by distance by Sydney. However, the girl comes back and discovers Vaughn/Michaux and the open safe and releases the alarm. As they are running in separate ways to the extraction point, Sydney receives a phone call from the hospital doctor. Once Vaughn/Michaux joins her, she announces him that she is pregnant. They then jump from the edge of the cliff to the sea with a parachute.

CIA prison: Jack visits Sloane who asks to be released in order to help his ill daughter Nadia. Jack asks about 3 off-book trips Vaughn made. They match locations and timeframes where Le Corbeau (The Raven) aka Renée Rienne also was. Sloane says that Rienne is wanted for the assassination of a Turkish interior minister in 2001, and the murder of three CIA agents in Serbia. He urges Jack to tell Sydney.

Unknown location similar to APO: One of Dean's employee, a young blond female, cracked Marshall's savant encryption. She explains to Dean that Vaughn had many aliases and that one of them passed the Italian customs the previous night.

In a car, close to train tracks of an Italian train station: Sydney and Vaughn/Michaux, waiting for Lehman, discuss her pregnancy. Vaughn/Michaux says that he thought they would wait to be in safer situation, but when he sees her and thinks of the baby, he can't wait to meet it.
Lehman arrives and waits for Vaughn/Michaux behind a stationed train. Vaughn/Michaux goes to meet him with the book; Sydney stays in the car. Vaughn/Michaux hands over the book to Lehman. As the transaction takes place, two cars approach them and from one of them emerges Dean. As Sydney wants to see more, a train passes between her and the scene where Lehman, Vaughn/Michaux and Dean are. Dean kills Lehman who was trying to escape. As the train conveys platform wagons in its last part, Sydney witnesses, powerless, the helicopter co-pilot getting off the second car and shooting Vaughn/Michaux in the chest with a machine gun. Dean takes the book from under Lehman's body and takes off with the helicopter co-pilot. The train is finally gone and Sydney joins Vaughn/Michaux who seems to be in a very bad shape.

Italian hospital: Vaughn/Michaux is in surgery and the situation does not look good. Jack tells Sydney that her integrity can be stained because of Vaughn's actions and contacts with René Rienne, to which she answers that she is expecting his child and that there must be an explanation. As Sydney goes to see Vaughn/Michaux coming out of surgery, Jack receives a call from Marcus who says that Dean was not in Special investigations and disappeared 3 years earlier, presumed dead. He tells Sydney Sydney about Dean.

APO: weiss, Marshall and Marcus plan an extraction for Vaughn, once he gets stable.

Italian hospital: Vaughn/Michaux and Sydney discuss baby names and profess their love. As she leaves to let him rest, he crashes and does not respond to resuscitation efforts from the medical staff. Sydney remains speechless, all the time, even when Vaughn/Michaux's is removed.

Back in the States: we witness the funeral; Marshall, Weiss, Marcus and Jack are some of the coffin bearers. Sydney witnesses them putting the coffin in the hearse, silent.

London: Sydney, wearing a brown short hair wig enters a pub and meets Renée, who is bartender. At first, she denies her identity until Sydney mentions Vaughn's name. She tells Sydney she should not have come to her, to which Sydney calmly answers that Renée does not know her very well.