A Free Agent
Sydney tells Vaughn that it's her graduation day, and he quickly realizes that she wants to quit the CIA. Kendall doesn't want to accept her resignation; he tells her that if she leaves she will forfeit her clearance to see her mother. Sydney visits Irina and tells her the situation; Irina doesn't want Syd's decision to be based on that and she tells Syd that she will refuse to see her if she remains with the agency. Later, as Sydney is preparing for the graduation ceremony, she receives a call from Sloane who reveals that he provided her with the information that brought down the Alliance. He says that they have set each other free and he warns her not to come after him. At the CIA, Syd learns that Sark has kidnapped a mathematician named Neil Caplan, and Jack reasons that Sark is still working with Sloane. Jack deduces that they want Caplan - a specialist in Knot Theory - to help put the Rambaldi artifacts together. Marshall, who is thriving in his new job with the CIA, is able to find a lead on Sloane, and Syd and Vaughn go undercover to find information about a cargo plane that Sloane may have used. Dixon learns from Syd that the CIA wants to offer him a job, but he feels betrayed and tells her that he never wants to see her again. The data from the plane leads Syd and Vaughn to Switzerland where they rescue Caplan's family, who were also kidnapped to ensure Caplan's compliance. Using the kidnapper's phone, Marshall pinpoints a call to a Zurich bank. Syd and Vaughn race to the bank, where Sloane in disguise is in the process of stealing a device that Caplan needs to assemble the Rambaldi device.. In the bank's lobby, Syd spots Sloane and draws her gun. Vaughn follows suit, as do Sloane's henchmen. Sloane tells him that the building is rigged with explosives and if he is not allowed to leave, the explosives will be detonated. Syd and Vaughn reluctantly lower their weapons. Sloane throws the car keys to Syd and announces that she will drive him away from there.
Sydney: I'm graduating today.
Vaughn: What? When the hell did you have time to take a class this year?
Sydney: I wasn't even going to go to the ceremony but... And I've been lying here remembering why I never gave school up and why I killed myself writing papers instead of... I don't know, accepting that I'd be an agent forever.
Vaughn: You're going to quit the CIA, aren't you?
Sydney: I've had two years of perspective! I am through letting Arvin Sloane control my life and I don't need your approval to resign! I told you as a courtesy!
Kendall: Well, then, I will pay you the courtesy of informing you that if you leave this agency, you forfeit the clearance to see your mother.
Sydney: I'm thinking about leaving the CIA. Which would mean giving up my clearance to see you.
Irina: You're too forgiving, Sydney. Don't pretend I'm something I'm not. I've never been a real mother to you and... you don't owe me a second chance. If you make this decision about me, you're a fool. In fact, if you decide to stay I won't agree to see you anymore. Take care of yourself.
(on the phone)
Sloane: Congratulations, Sydney. You have so many things to celebrate today. I, myself, am still coping with the pain and disappointment of learning that you and Jack were double agents. The two people I trusted most in the world.
Sloane: You don't really think it was a coincidence that I happened to be away these past two weeks, do you? The intel that you acquired that allowed the CIA to take down the Alliance -- I provided that. My involvement with the Alliance is merely a means to an end.
Sydney: Why are you telling me this?
Sloane: Because knowing that I'm alive is going to tempt you to come after me. Don't. We've helped set each other free, Sydney. And as much as I wish you well, I will end your life if you get in my way.
Jack: Simply put, it's the study of geometric objects and how they fit together. All Alliance facilities have been raided yet we haven't found a single Rambaldi artifact. If Sloane was expecting our raid, he could've had everything moved to a secure location. He must be using Caplan to help him assemble a Rambaldi device.
Vaughn: So what happens when Sloane puts the pieces together?
Jack: Whether or not you believe Rambaldi was a prophet, he did anticipate technological advances, many of which seem most applicable to warfare. It's likely Sloane is building a weapon.
Caplan: I don't understand. Why do you want me? I'm nobody.
Sloane: You're going to help me put them together because, you see, Mr. Caplan, I know that you feel like you're only a hostage right now. But I assume you became a scientist to discover what secrets the universe has to offer. Believe me, when we're done here, you'll be thanking me for giving you the answer. So why don't you go ahead and take a look?
Dixon: How long have you known?
Sydney: Two years. I wanted to tell you so many times, but I was ordered not to. The CIA had no way to verify what I knew in my heart was true -- that you would never consider working for a man like Arvin Sloane.
Dixon: We were partners. You lied to me, then chose to tell me the truth when it was convenient for you. I never want to see you again.
Sark: I made contact with our point man. He's assembling a team for the bank but I must question your decision to lead them in yourself. In spite of your precautions, it's wildly risky, given your new level of notoriety.
Sloane: I'm approaching the finish line of a thirty-year odyssey. I won't let anyone else take the final steps for me.
Sloane: Ah... you must be the man that Sark told me about. The man that Sydney was willing to kill me for.
Vaughn: She would have killed you for a lot less.
Considering what was happening in the characters' lives, the title for this episode is especially clever. Sydney thought that she was finally released from all of her obligations as a secret agent, but she realized that the battle doesn't end. Dixon, trying to recover from betrayal by Syd and SD-6, is honest with his wife, and she is equally honest in saying that she'll leave him if he accepts the job with the CIA. Sloane stated that he and Syd have set each other free, and although he no longer answers to the Alliance, he is still living a life of deceit and lies.
Ironically, it was the source of Sloane's initial freedom from the Alliance - the high-tech genius - that also gave the CIA a clue to finding Sloane. He always seems to be one step ahead of the game, so it's quite possible that he knew that the tech-guy's fake eye would lead Sydney to him. I was trying to decide if Sark's declaration that Syd was in the lobby was one of surprise or one of satisfaction that the plan was working.
The title of the episode could have a second meaning for Sloane, who has apparently been working towards his own agenda for the last thirty years. And where have we heard another mention of "thirty years" on the show? Correct: when Irina said that she had waited almost that long, presumably to see Sydney again. I know I keep saying it, but I'm confident that Irina has her own hidden agenda. It may be bad, it may be good, or it may be that I'm falling for a plot by the writers to throw us off of their real plan.