The CIA learns that Sloane has been missing for five days and has been replaced as the head of SD-6 by a man named Anthony Geiger. From Sark, Sydney learns of server 47, where Sloane had secret files stored; Syd rationalizes that it might have information that could be used against the Alliance. The CIA locates the mysterious server: it's on a plane that only lands to refuel. Syd uses a disguise to board the plane and get close to the computer expert that travels with it. She obtains the data, but Kendall is reluctant to move in on the SD cells since the information may be incorrect. Jack goes to SD-6 for a security code that would verify the info's accuracy. Geiger, who has been finding incriminating evidence on Jack and Syd, catches Jack trying to get the code. Jack calls Syd - no doubt under pressure from Geiger - and asks her to come to Credit Dauphine, but he uses a secret phrase that lets her know to stay away. As Geiger tortures Jack trying to find out who he's working for, a desperate Sydney asks Dixon to meet her. She tells him that SD-6 is part of the Alliance, not the CIA, and she implores him to get the security code. He dubiously considers what she told him, then finds the code and sends it to her. It matches the one given in the Server 47 data, and Kendall orders an assault on the Alliance. Syd joins the attack on SD-6 and finds Jack just in time. As the CIA gains control of the facility, Vaughn and Syd find each other and kiss passionately. Elsewhere Sark, who has escaped unharmed, calls Sloane and tells him that phase one is complete. Sark then phones a Francie look-alike who reports that everything is in place, as we see the real Francie: dead.
Vaughn: I think you know what.
Sydney: I need you to tell me.
Vaughn: You need me to tell you what? That when you're on operations, I can't sleep at night. That when we're in debrief I have to force myself to remember what the hell we're supposed to be reviewing. When all I want to do is kiss you.
Sydney: Excuse me. Sloane's being replaced?
Kendall: He's been MIA for five days. With Sloane gone and Geiger coming in, we no longer have access to their inner circle. So, Sydney and Jack, your assignment is to get close to Geiger, earn his trust, get back in that inner circle. That's it.
Sark: The new boss has a dreadful personality, don't you think?
Sydney: I've seen worse.
Sark: Am I supposed to take that personally?
Sydney: There's only one reason Sloane would keep secret the existence of a computer. Because this computer server forty-seven is a vulnerability.
Jack: Until you tell me what you're suggesting, I have nothing to respond to.
Sydney: I think there's a central Alliance computer: I think that's what server forty-seven is. A network that links all the SD cells. It makes sense, doesn't it?
Vaughn: We tracked down server forty-seven. The reason you couldn't get a twenty on it is because it doesn't exist on this planet. It's in the sky. It's a 747 purchased by the Alliance in 1998. They retrofitted the interior to contain a secure server and a satellite uplink.
Will: Okay, the suspense is killing me. What's the occasion?
Francie: The restaurant is actually making a profit.
Will: After only six months? Is that even possible?
Jack: The answer is in the document. According to the information you retrieved, each SD cell uses a code which changes weekly to operate their security system. The current code is listed right here.
Vaughn: So you're saying we need to get into SD-6 and find out what the actual code is right now?
Sydney: If it matches the one in the document, then the rest of the intel is real.
Kendall: In which case I could go to Langley about raiding the Alliance facilities.
Vaughn: Do we have the current SD-6 code?
Jack: No. But I can get it.
Vaughn: Did he get the code? Syd?
Sydney: He was compromised.
Sydney: He just said "Take surface streets, they're doing some work on the freeway."
Vaughn: I don't understand.
Sydney: It's a phrase we came up with last year. A code to let one of us know if the other was ever discovered, to warn them to stay away. He's with Geiger now.
Dixon: No, this does not MAKE ANY SENSE!
Sydney: YOU HAVE TO LISTEN TO ME! I can't go back there or they will kill me too! We need you to go into SD-6. We need you to hack into the system and make visible a hidden file, one that you would never see, never know was there. It's a code. A number that we need. If it's a match to one we already have, it will confirm the data and the CIA will raid SD-6 and every Alliance office! If you follow these instructions to get the code you will be in the core of the SD-6 computer network and you'll see ... it's not CIA. It's Alliance. I'll wait for your e-mail but you need to hurry.
Sark: Sydney leaked the intel to the CIA and the rest played out exactly as you predicted it would. So congratulations, sir. The Alliance is gone.
Sloane: We shouldn't celebrate yet. As you know, there's much more work to be done.
Sark: I just wanted to let you know that phase one is complete.
After seeing this episode I was amazed yet again that some people don't watch Alias because they think it's predictable. This was without a doubt one of the most unpredictable hours of television that I've seen in a long time.
For starters, who - besides those that read spoilers - would have guessed that Vaughn would confess his feelings for Sydney, right there at CIA headquarters before an important meeting? (Then again, where else could he talk to her like that? When they're out in public and can't make eye contact? I think not.) The fact that their conversation was interrupted is quite representative of their entire relationship: just as things get interesting, duty calls.
Second, although TV Guide said that Geiger would be suspicious of the Bristows, I didn't expect him to be so open about it. He seemed to have Kane's attitude that he didn't need proof, just a hunch. His initial question to Sydney was a reasonable one: why *would* someone work for an organization that murdered the person they loved?
One of the most surprising developments was that the CIA succeeded in overthrowing the Alliance. Usually in shows where the main character is seeking revenge/justice like Sydney was, the goal is rarely achieved since it would signify the end of the quest and the end of the series. But in typical Alias style, they've challenged that old way of doing things and completely changed the lives of the characters.
I knew the episode's title was Phase One, but I didn't think about the implications of that, namely that what happens here is just the beginning. Sloane is a much more formidable opponent than most of us - including Syd and Jack - realized. Geiger wasn't the only one who noticed the "red flags" in their files. Sloane knew they were double agents, and he used them to accomplish his own objective.
His grand scheme also required the loss of Francie's life. I know it's just a TV show, but does anyone else feel like they've lost a friend?