Fake Francie tells Sark that the CIA is on a mole hunt; Irina doesn't want Will killed, but she does want him to be convincingly framed. The setup works as Jack and Kendall believe that Will is the second person who was genetically reprogrammed to look like someone else. Even Sydney has her doubts that he isn't a fake. Believing that Francie needs to be protected, Syd tells her that she works for the CIA. In an effort to find more info about the second double, Syd and Vaughn follow a lead that reveals the location of the data they seek. Meanwhile at the CIA, Kendall arranges for Will to be transferred to another location for unrestricted interrogation; Sark sets up an ambush so that Will can be extracted and killed. The attack doesn't go as planned, and Will is able to escape. Jack is approached in a very public place by Sloane, who says that he forgives Jack for his betrayal at SD-6. He also wants Jack to consider returning to their partnership. Jack refuses, but Sloane leaves vowing that they will work together again. On a second mission, Sydney goes to get the data that can exonerate Will, but Irina gets there first. She erases the data, telling Sydney that she will have to help her in order to get it. Elsewhere, Will has called the only person he thinks he can trust: Francie. She picks him up and drives away.
Fake Francie (on the phone): Will Tippin may be compromised.
Sark: Our superiors deal in absolutes. Either he is or he's not.
Fake Francie: The CIA is on a mole hunt to find out who accessed the defense satellite communications system. It's only a matter of time before they trace it back to Tippin, and then to me.
Sydney: I have known Will for years. Trust me on this.
Jack: There's another possibility... that the man we have in custody is not Will Tippin. Project Helix. The doubling prototype that you destroyed in Poland was designed to reshape a person's physical attributes to identically resemble someone else. The prototype's database revealed two scheduled recipients of the procedure: Dr. Markovic who was killed, and a second unknown individual.
Sydney: You think Will is the double.
Kendall: We found Provacillium in Will's car. It's a medication usually taken by gene therapy patients to keep the body from rejecting the DNA mutations.
Will: What was that eye scan?
Sydney: It's a test. It analyzes your retina. Someone who's been doubled develops proteins. They're like markers. They found proteins.
Sydney: If someone wanted to set Will up, this is exactly what they would do -- plant these clues, condition him. I'd like permission to assign Francie protective detail. If Sloane is targeting my friends, she could be next.
Sydney: I'd also like to speak to her about Will. She might have information that could help.
Jack: Tell her what you think is necessary, but only what's necessary.
Fake Francie (on the phone): I intercepted a DOJ transmission. They're moving Tippin to a more secure location. Once he's there he will be unreachable.
Sark: Organize a team to intercept the transport and extract him. To the CIA, this will confirm his value to us.
Fake Francie: And once we have him?
Sark: Kill him.
Jack: Sydney, you have to accept the possibility that the man we have in custody is not your friend.
Sydney: Dad, I don't believe it.
Jack: I understand.
Sydney: 'Cause if it wasn't Will then Will is most likely dead and I can't handle that.
(Sloane joins Jack at his outdoor table at a restaurant.)
Sloane: It's good to see you, Jack.
Jack: I assume that since you're sitting across from me with so little regard for your life, I'm in the cross hairs of a sniper rifle.
Sloane: Two of them.
Sloane: I'm curious, Jack. When did our friendship end?
Jack: The moment you recruited Sydney over my objections.
Sloane: Ahh. I thought so. If I had known that decision would cost me our friendship and my relationship with Sydney, I would have done things differently.
Sydney: You erased it...
Irina: I transferred a copy to a secure location. I'll give it to you. In exchange, I want you to do something.
Sydney: Go to hell!
Irina: If you don't, you'll never clear Will's name. He'll be tried as a traitor and executed. I'll be calling on you soon, Sydney.
To quote a line from my other favorite show: "As far as evil plans go, it doesn't suck." The plot to frame Will as the second double was a pretty believable one, but one has to marvel at the resources possessed by the bad guys. On a lesser level, it's also a bit surprising that the CIA did not recognize that he was being set up. Then again, if they had believed Will, this episode would have had to fill most of its time with something else.
Will told Sydney that he can't trust her and that meeting her destroyed his life. Given what he's been through it's understandable that he'd be more than a little upset, but has he forgotten what brought him into Syd's world in the first place? It was his own insistence in investigating Danny's death.
Kendall said that he wanted Will transferred "to protect Sydney", and Jack seemed to recognize that as Kendall's motive. Since when does Kendall care about Sydney? I'd say that Kendall's motive was a desire to get back at Jack for taking his job, and that motive just happened to line up with the evidence that Will really was the second double.
The scene with Dixon and Will revealed how much Dixon was trying to suppress his personal feelings and do his job. Although he believed Will was the one who murdered his wife, he knew Sloane was the cause of her death, and Dixon was willing to work with Will to get to Sloane. The fact that Dixon could have killed Will, but didn't, reflected the extent to which he was controlling himself; this is another example that Dixon is an excellent agent.
Fake Francie was even more fake than usual in this episode, which made her *really* annoying. Her fake tears, and her fake concern for Will ... we can only assume that Sydney's concern for Will has completely blinded her.
Sloane's visit to Jack was arguably the most surprising part of the episode. To those that didn't know the circumstances, the scene looked like a simple meeting between two old friends. As if all their past issues aren't enough, now Sloane has made a new discovery about Rambaldi. Great - that's just what we needed. Sloane's vow that he and Jack will work together again soon was sufficiently creepy. Knowing Sloane, we can be sure that it was more than an idle threat.