The vial of tissue is removed and a photo taken. Various people are analyzing it. The box is closed and put into a case. Syd asks Marshall if he's analyzed the cube. Marshall says that they are here. They are taking the cube away. Their jurisdiction supercedes theirs. Syd goes to ask them what they are. They are DSR. They won't tell Syd what it is or where they are going. Syd tells her father that it isn't fair. Every time they get close something happens. Jack tells Syd that the order to remove the cube comes from Langley. They can't bring Dixon in yet.

Syd reviews a file. She hears a noise and gets her gun before investigating. She goes out into the hall and is shot with a dart. A plane takes off. Syd wakes on the plane. Kendall is on board the plane. He tells her he is sorry they had to do it this way. She asks if he is part of it. She asks if he is covenant. He says no. He is with special research. His team was ambushed in transport of the cube. Syd says the covenant got the cube. She asks what that has to do with her. He says that it has everything to do with her and tells her they need to talk about the last two years. She says she has no recollection of the last two years. He says he does remember. She says you have known all this time and asks why he didn't say anything. He tells her that she asked him not to.

Syd places her hand on a scanner. She has to be authorized to get info on her own life. Kendall tells her she died or at least they believed she did. The existing DNA matched her own. He watched Vaughn spread her ashes. Nine months later he got a call from her saying she escaped from the covenant and wanted to turn herself in. He met her at a safe house in Tuscany. She didn't look like he'd ever seen her before.

She shot her three times. And she passed out. She was dead to the world. When she woke up it was days later and she was strapped down in the back of a van. She wakes with duct tape on her mouth and a man tells her that they will work together. He will get the results that his employer wants. He injects her with a neurotoxin. It paralyzed her. She could only watch. They exhumed her roommate and left the body. Then they extracted pulp from her teeth and left it in the body that was there. To them it was her. We see footage of Syd's funeral at the beach. A haggard Vaughn embraces Weiss. Syd is in the back of a van watching. He tells her he will move on. The sooner she accepts who she is the easier it will be. Sydney Bristow is gone. Syd asks why she doesn't remember. Kendall tells her they will get to it.

Kendall shows her a photo of Oleg. Syd says she killed him. He had answers and died. She asks what he did to her. The covenant believed that she was critical to their operation. He was using brain washing techniques on her. Sensory deprivation, shock therapy, put her out with a sedative in one arm and shock her awake in the other. They took away her id. They gave her narcotics, withheld food, and bombarded her with information. They gave her a past. Told her she became a contract killer. This went on for six months. At this point Oleg thought his therapy was starting to work. Once Oleg believed she was ready they gave her a test to make sure she really believed she was ready. They introduce Julia Thorne to a panel. They give her a knife and tell her to kill this unimportant man. The man begs. She stabs him.

Syd asks Kendall who the man was. He tells her they don't know. She says so she was programmed. He says no, not by the covenant. Kendall tells her that as a child she was programmed by Jack. Syd says project Christmas. Kendall tells her that all the subjects were programmed with a fail safe to prevent them from being brain washed. Kendall says the man was in a Covenant facility. He was going to die. She must have known that. Syd says it doesn't lessen what she did. He tells her if she didn't they both would have been killed and he couldn't have contact her.

In flashback Syd says she wants to return home. She wants to see her dad. Kendall tells her that he is deep undercover. She can't return home. She will put the lives of the people she loves in jeopardy. The covenant left Will for dead. The covenant believes they have her programmed. If she doesn't return, they will come after her. She wants to see Vaughn. He tells her that she has been gone for nine months. She says he loves her, nine months is nothing. He lets her go. She returns home. Syd sees Vaughn with Lauren. She realized her presence was a danger to him so she did the only thing she could. She tells Kendall that she'll do whatever he wants. She became Julia. (Julia is a blonde by the way).

Kendall tells her they sent her to Algeria where she met Simon Walker. They started working together to get the cube. Syd kept Kendall up to date. Lazaray, like Sloane was obsessed with Rambaldi. That the cube contained Rambaldi's DNA. She went to see Lazaray and struck a deal. She tells him that unless he does exactly what she says he will be dead in 24 hours. She fakes Lazaray's death.

She asks where they are going. He tells her to his research facility in Nevada. He reveals that 2 years ago when he questioned her that he wasn't with the FBI, he was with Special Research (OMG I watched that on DVD recently and wondered what was up with Kendall being FBI in that and CIA second season!!!!!!!!!!!!!!!!!). She tells him that she has never heard of project Black Hole. He gives her a packet of info. A quarter of the artifacts they've collected have come from her. They believe that she is the chosen one. Syd says her mother said that the night she disappeared. Kendall says that four months ago she asked him not to tell her any of this. He held off as long as possible. He tells her that it took her 9 months but she found it. It was in Namibia in the fish river gorge. To Rambaldi's followers this was the Holy Grail. A mile long trek took them to a vault that hosed the cube. Lazaray has devoted his life to collecting the keys to the vault the last of which he found 2 weeks before their journey. Each key had a name on it that corresponded to a lock. Lazaray has to hold one of the keys to keep it open. The cave begins to collapse. Lazaray was trapped. Syd hacks off his hand. Syd gets the cube and gets Lazaray out. Syd was supposed to give Kendall the cube but she never showed up. Instead he got a disc.

She wants to know what happened to her memory. He inserts the CD into a device and tells her that she may want to sit down for this.

Syd is on the screen saying she's sorry he's expecting the cube and he gets this. She can't go on with the plan they had but she can't do it. It isn't safe with the CIA. Everything gets stolen. She's found a man who has done research with long and short term memory. She doesn't want to know what she's done with Rambaldi's DNA so she is having the last 2 years erased from the memory. She tells him that if she survives and doesn't remember don't tell her.

Syd asks why he is doing this. Kendall says that Rambaldi spoke of a second coming. Syd thinks they want to clone him. Kendall says no it spoke of a second coming by way of a child. Syd reads the prophecy about unseen marks etc. Kendall says that they believe that the DNA can be used to fertilize the egg of a woman known in the prophecy as the chosen one. Syd looks at her scar. That's why they cut her open. So they could fertilize her eggs. Kendall tells her that is why she didn't want to remember. Kendall got the disc two days before she reappeared.

Syd tells him that Sloane gave her an envelope with coordinates that lead her there. Once the covenant had that they didn't give up. They tricked her into getting it. They wanted her to lead them to it. Syd says there has to be someone else involved. Syd calls Marshall. She asks Marshall if he put a tracer on the cube because of what he said about wanting to know where they were taking it. Marshall says that he swears he didn't. Syd pleads with him. He says yes but you can't tell anyone I did because I am about to have a baby here (OMG - a BABY?!!!!!!!!!!!!!!!!!!!!!!! Could it be THE baby?????) Marshall can locate it to a ten yard radius. Sark has the cube. Scientists remove something from a tube labeled Sydney Bristow.

Kendall tells them they will be dropped into a facility in Patagonia. They have reason to believe the fertilization will happen tonight. Syd goes to talk to Dixon. She asks what he is doing. Dixon tells her that she was there that day when Kendall got the call. He knew. He was under orders not to tell her. He tells her that it was difficult. He knows what it must have been like for her at SD-6. He is going with them. It is personal.

The team jumps from the plane. They enter the facility. Dixon tosses in a smoke grenade. The team rushes in. A gunfight ensues. On a screen it appears that we can see the fertilization - I think. Or perhaps two eggs. The gunfight stops. Syd and Dixon stare at the equipment. Dixon says Kendall wants it all brought back for analysis. He steps away and says do your thing. Syd sets fire to the whole mess - including the vials with her name on them. (No idea what happened to Sark in all this). Lazaray is brought out. He calls her Julia.

Sark is on a cell phone driving away. He says they have his father. Take care of it and hangs up.

Syd talks to Lazaray. He asks if she knows about the passenger. The ambulance arrives at the hospital. Syd gets out. They remove Lazaray. Lazaray is shot. He is dead. A sniper has shot him. The sniper is LAUREN! She phones and says the matter is taken care of. Then says yes sir I will.