When Dixon asks Sydney how long she's known the truth about SD-6, Sydney says "two years". This is a serious time-line issue because in the previous episode Sydney tells agent Lennox that Danny was killed "last year", and seeing as how Danny was killed 3 months before Sydney found out the truth about SD-6, this "2 year" time line is impossible.
Number 47: During the briefing at the CIA, Jack displays an ID card of Neil Caplan that expires in (20)07-14-04 (14-04-07).
Number 47: The magnetometer Sloane took was kept in box 4747.
It is established, that the Rambaldi Journal is written in Italian and encoded, or else CIA and SD-6 wouldn't have to decipher the pages first, as seen in various episodes of season 1. However, the "gifted" mathematician seems to have no problems in reading the original documents.
A few things about Zurich/Switzerland:
1. In Switzerland vehicles have a license plate on the front, but the ones shown in the episode are on the back of the cars. The front only has the number and the two letters for the "state" without the flags.
2. The interior of the bank looks not like a typical Swiss bank, more like an American bank.
3. The streets shown during the car chase do not look like Swiss streets. In Switzerland the line is white, not yellow/black. The traffic signs shown are not "Swiss" ones. Except for the skyline it is obvious nothing was shot in Switzerland.
Sydney and Michael are in a bank trying to get to Sloane, aiming their guns at him while his bodyguards are aiming their guns at Sydney and Michael. But Sydney's finger isn't even on the trigger, which is odd, given the circumstances.
Mercenary: (to Vaughn) If you would've simply told me that the CIA was interested in my client list I would have told you to go make love... with your mother.
Sydney: (About Sloane) He planned for this, he wanted The Alliance gone, and this family he's taken hostage, these are not the only people whose lives he'll destroy... (With frustration in her voice) this is never going to stop.
(Sloane calls Sydney to congratulate her for her graduation)
Sloane: Our first honest conversation Sydney, and you have nothing to say.
Sydney: Listen to me you son of a bitch, you have been a plague on my life, you repulse me. Every time I sat across from you to listen to your lies, all I could do is fantasize about slashing your throat.
Sloane: Well I can't pretend to be surprised you feel that way, my only hope is that you can learn to forgive me.
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.
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 consciously work 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.
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 answers. So why don't you go ahead and take a look?
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.
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.
(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.
Sydney: I'm thinking of 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.
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: What? Are you blackmailing me?
Kendall: Civilians aren't authorized to be in this facility, let alone have access to a terrorist that we can't even acknowledge is in our custody. In or out kiddo - can't have it both ways. (Kendall walks away)
Jack: Legally he's right... ethically he's an ass.
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 just... I don't know, accepting that I'd be an agent forever.
Vaughn: You're going to quit the CIA, aren't you?
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.
(After his debriefing, Marshall accepts a job with the CIA)
Vaughn: Marshall, I'm Michael Vaughn, welcome to the CIA.
Marshall: I've heard that one before.
Vaughn: Well, this time's for real.
Christian Slater is billed as "Special Appearance By".
Music from this episode includes:
"My Sundown" by Jimmy Eat World
"I Can't Forget" by Evan Olsen
"Get Free" by The Vines
Fight sequence that resembles Raiders of the Lost Ark: When Sydney fights a man in front of a plane, and knocks him into the propeller.