
Episode 8 - Passage, Part 1
The episode opens with Sydney confronting Sark on their way to SD-6 the morning following his appearance there. She reminds him that he can't reveal her part in getting him to Sloane without revealing his own duplicity in the matter. Sark assures her that he won't betray her.
Sydney and Jack meet later to discuss what Sark and Sloane's possible agenda might be. Jacks admonishes Sydney to think about the fact that only a few weeks ago, her mother turned herself into the CIA... just days ago, Sark made a backdoor agreement with Sloane. He points out that the likelihood of coincidence in this matter is small. Also, he points out the danger that Sark might know she is a double agent.
Sydney goes to see Irina to find out if she'd ever mentioned that she was a double agent for the CIA. Irina says no, and questions Sydney about the intelligence Sark had provided Sloane thus far. Sydney explains the debriefing she'd had that morning when Sloane informed everyone of Sark's cooperation. According to Sark, a set of communication codes for the Uzbekistan Ground Forces has fallen into enemy hands. An associate of his has acquired the codes, and they've arranged for him to sell the codes to Sark. Sloane assigns the op to Sydney and Dixon, stating that they will be posing as Sark's associates, as it would be disastrous if these codes fell into the wrong hands.
Sydney doesn't believe that's all there is to the story and asks Irina what the codes might really be for. Irina tells Sydney she must be allowed to leave the facility for forty-eight hours and agrees to a Special Forces escort, but she won't explain why. Sydney presents the idea to Kendall who refuses. Vaughn assigns her counter-mission, and she returns to SD-6. Sydney and Dixon go to Uzbekistan and successfully obtain the communication codes. She dead drops a copy of the codes to the CIA.
After her return to Los Angeles, Syd and Vaughn are talking, and Vaughn shows her a watch that had belonged to his father. He explained that his father had said that you could "set your heart by it". Vaughn goes on to say that the watch had stopped the day he met Sydney... October 1st. Their conversation is interrupted by pages from Kendall, summoning them both to the JTF.
Kendall explains that the communication codes she'd acquired in Uzbekistan were actually the control codes for six suitcase nuclear warheads that had been stolen earlier. Sydney reminds him that Irina had warned them something awful might happen if they didn't listen to her. The team goes to her cell, and she tells them that she does know where the nukes are located... under a former prison in Kashmir. Kendall orders her to lead a team into the prison to recover the nukes, but she refuses. After a heated exchange, Sydney makes everyone leave, and she convinces her mother to help... much to Jack's dismay. He tries to prevent Sydney from going on the mission, but she challenges him to join them instead.
Jack outfits Irina with a necklace laced with C-4, which is meant to ensure that she doesn't try to escape. He warns that if she does try anything she shouldn't, he'll detonate the necklace and kill her. The three Bristows leave for India and successfully meet up with their in-country contact. Unbeknownst to them, he has been compromised, and the rebel group that controls the facility in Kashmir intercepts them, killing the contact. Before they can be executed, Irina makes a silent plea to Jack to deactivate the necklace, so that she can use it as a diversion in order for them to gain control of the situation. He agrees, and after she throws it into the midst of the rebel group, he detonates it, using the explosion as cover to gain control of a few weapons. After a gun battle, the Bristows kill all of their rebels, but are left on-foot, with no supplies, and no immediate way to contact the CIA for extraction.

Episode 8 - Memorable Irina Quotes
"I'm going to ask you for something you have no reason to give... I'm going to ask for your faith."
"I cannot give you details, because I don't trust the CIA. They almost had me executed two weeks ago! The only way for me to maintain my value is to tell you what you need to know to stay ahead of Sloane, and all you need to know now is that if I'm not allowed to leave, everything you've worked to accomplish will be lost."
"I have cooperated, Agent Kendall. You didn't listen."
"You're so willing to take risks for your country. Why aren't you willing to do the same for your own happiness?"
"Jack, Sydney's smart, and she's strong... but she's not happy."
"I knew it the moment I saw her... I'm her mother."
"I'd offer to go first, but I don't want to be accused of trying to escape!"
"The only reason you know about the nukes is because of me. I want some respect!"
"Jack, we're in enemy territory, and the PRF knows we're here. We need to start trusting each other... right now."

Episode 9 - Passage, Part 2
All hell breaks loose at the JTF when the C-4 necklace is deactivated and a combat is detected. After the explosion, the team loses contact with the Bristows. Because of the clandestine nature of the operation, Kendall deems it a dismal failure and determines that regardless of their status, the Bristows are on their own. Vaughn makes a plea to investigate their whereabouts quietly. He receives an Echelon intercept that the rebels plan on activating the nukes the next day.
As the Bristows are walking through the foothills, they pause to treat a deep scratch on Sydney's leg. Irina suggests that her own contact is closer than Jack's... he is reliable and would have the equipment they required to infiltrate the facility. Jack refuses, because he doesn't trust her. After a brief power struggle, he stalks off, leaving Irina to make one more plea for assistance with Sydney. Sydney doesn't go against her father, and they resume their trek. The come to a train and are able to stow away in a baggage car, finding food and cheap Indian rum. While drinking, Jack and Irina reminisce over a funny, but particularly happy moment from their marriage, when Sydney was a small child.
After they reach Srinagar, Jack's contact informs them that he might not be able to assist them as Jack had hoped. His main supplier had died a few months prior, and all he has is basic weaponry and the means to provide them with aliases and transportation. Irina is visibly frustrated, because due to Jack's earlier stubbornness, they will not have everything they need when they get to the facility. While they are changing, Sydney uses the satellite phone and calls in to Vaughn, who informs her that the nukes are set to be activated by the rebels. She can deactivate them, because she'd acquired the control codes for SD-6. As she hangs up, Jack and Irina get into another argument over the contact's truck, which has only a foam filter that Irina knows will not withstand the desert conditions. Sydney interrupts their bickering and sets them straight on what they need to do from that point forward. They leave, with Jack stowing Irina away in one of the grain bins in back of the truck, as she's the most likely to be recognized. After several hours, the truck does indeed overheat, and they are forced to move ahead on foot. Irina asserts her right to take control and leads them through a minefield to the sewage tunnels and into the facility itself. While walking through the minefield, they encounter enemy fire, and Jack takes a hit to the vest while tossing a gun to Irina. He lands on a mine, and Irina must work with Sydney to disarm it.
Once they reach the facility, Irina outlines what each of them need to do in order to gain access to the lab where the nukes are most likely being stored. Her plan requires them to separate, which Jack protests. He doesn't trust her, and states that she'd been an officer in the facility, so if she wanted the nukes for herself, she had friends there to help her. She informs them both that while she'd been there, she'd been a prisoner, held by the KGB for suspected treason. She insists that they follow her plan or turn back. Jack reluctantly agrees, and she promises to meet them in the lab in five minutes.
When she doesn't arrive, Jack and Sydney get to work recovering the nukes. They are interrupted by the rebel leader, Gerard Cuvee and taken hostage. Irina is with him. Cuvee puts Jack and Sydney into separate cells, and then he and Irina interrogate Jack... hitting him a few times to make him talk. Cuvee is called away, leaving Irina alone with Jack to finish the interrogation. She slips a key into his hand and explains that she had been caught by Cuvee earlier and was trying to keep them all from being killed. She explains what the rebels are up to... they aren't detonating the nukes, but using them to open a Rambaldi artifact... and how Jack and Sydney can contact the CIA for extraction.
Meanwhile, the CIA learns that India has become aware of the stolen nukes and is planning air strikes on the facility. Vaughn flies over to appeal to a friend of his in the Indian armed forces to hold off until he can extract the Bristows. The friend refuses, but gives him a helicopter and pilot, along with a head start, to make the extraction.
Jack and Sydney get free and contact the CIA in Los Angeles, learning of the impending air strikes. Kendall orders them out, but Jack refuses, saying that he's not leaving until they get Irina. They head to the lab and watch as the artifact is opened. The facility is bombed, and rebel personnel scatters. In the confusion, Irina takes a shot at Cuvee, and Jack rushes to her assistance, knocking him out. They recover the nukes and the artifact and rush outside, just in time to meet Vaughn and get extracted.
Upon returning to her cell, Irina explains to Sydney that she'd shot her in Taipei because Cuvee had been watching. That action was the only one she could take to maintain his trust and allow Sydney to escape.

Episode 9 - Memorable Irina Quotes
Jack: "I know what you're thinking."
Irina: "Do you?"
Jack: "Toaster."
Sydney: "What are you guys talking about?"
Jack: "We used to have this toaster at home. It was broken, and using it one night, I started a small fire."
Irina: "We had something...like this...to drink, and we both had a little too much..."
Jack: "I forgot about the toast I was making."
Sydney: "When was this?"
Irina: "You were... four years old? There was so much smoke... we had to move out for a week. We stayed in that hotel..."
Jack: "The Summit."
Irina: "The Summit."
Sydney: "Wait... was that the hotel with the sundaes?"
Irina: "Mhm."
Jack: "Yeah... I think you had one every night."
Irina: "We don't have the equipment, because your contact didn't come through. I know where the mines are planted."
Jack: "You want to walk through a mine field you haven't seen in nineteen years and assume no new mines have been planted?"
Irina: "I just spent five hours in a grain bin. It's my turn now. Let's get to it."
Sydney: "Where did the PRF get all these mines?"
Irina: "You Americans have the worst inventory controls in the world."
Irina: "So Sydney... how's school?"
Sydney: "I am writing my dissertation... supposedly."
"Don't move! You're on a mine."
"Friends? You know what this place was when I was here, Jack? A prison... where the KGB interrogated suspected traitors... and no, I wasn't an officer here. I was a prisoner. Why do you think I learned the sewage tunnels or memorized the mine locations? So I could escape, you idiot!"
"Trust me on this. If you don't make it out, I'm sorry this happened."
Irina: "You must have a lot of questions."
Sydney: "Yeah."
Irina: "One thing that should not wait any longer is why I shot you in Taipei. The rebel leader, Gerard Cuvee... when you were in Taipei... he was in the next room, watching... to see if I would betray him or you. Shooting you in the shoulder... giving you time to escape... it was the only way I could think to maintain his trust and keep him from killing both of us. We're both tired. You should get some rest."
Sydney: "You too... Mom."

Episode 10 - The Abduction
The episode begins with Sydney talking to Will and reflecting on what it was like to be alone with her parents again for the first time. She explains that she found it comforting to work with them, despite the crazy circumstances involved in their trip to India and Kashmir. Later, she goes to see Irina, who is walking around outside in the prison's recreational area. Irina tries to explain to Sydney why she joined the KGB. In an emotional scene, she tells Syd that she was foolish to think that anything could come before her daughter. They hug for the first time in over twenty years, only to be forced to separate at gunpoint by the prison guards.
Due to the failure of their operation in Kashmir, Sloane accuses Sark of betraying him. Under the threat of torture, Sark tries to assure Sloane that this was not the case. He reveals the location of an Echelon access terminal belonging to Gerard Cuvee, and they devise a scheme to steal it. Sloane tasks Sydney with accompanying Sark to Paris to retrieve the terminal as it is being moved to a more secure location. Her counter mission involves her downloading a secure deletion program to the terminal that would destroy it, but make Sloane think Cuvee had installed a failsafe.
While on her assignment with Sark, Jack goes to see Irina in order to offer her a deal in exchange for a confession. He believes that she and Sark have coordinated their efforts to infiltrate both the CIA and SD-6, and he promises her release from her cell into a secure private residence if she'll tell the CIA why she really turned herself in. As they are talking, Irina brings up the idea that they might still be legally married. Jack leaves her to consider his offer.
After realizing that Cuvee's Echelon terminal is useless, Sloane and Sark learn of another possible means to acquire the software. Sark explains that Cuvee had leased space in a data storage facility in London, and it was quite possible that he had a copy of the software stored there. Sloane assigns Sydney to go and retrieve a copy of the data. However, because the facility's security is so heavily encrypted, it requires someone with the ability to hack into the system on-site... Marshall is the only one who can do this, so it becomes necessary for him to go to London with Sydney.
The CIA is concerned, because they know that if Marshall sees any part of the code, he will be able to recreate it for Sloane. It is decided that their only option will be to "extract" Marshall from SD-6 upon his return from London. The CIA will take him into protective custody, and Sloane will think he simply disappeared.
The mission to London is successful, and Sydney and Marshall separate at the airport, with Sydney believing he'll soon be safe in the CIA's custody. As Marshall is being intercepted, Jack is visiting Irina back at the JTF. He asks if she's considered his offer, and she says that she has nothing to confess. She'd thought about making something up to get out of her cell, but in truth, her only reason for turning herself in was to make up for past crimes. Jack reveals that he'd investigated the possibility that they might still be married, and although their marriage was based on a lie, they were still legally married. Before he leaves, she tells him that she'll agree to answer his questions from now on, whereas she'd previously only agreed to speak with Sydney.
Vaughn is watching their interaction on the security monitor, and as Jack walks away, he gets a call that the CIA did not take Marshall into custody as planned. It is revealed that Cuvee's henchman, "Suit and Glasses", abducted Marshall in order to force him into recreating the Echelon software.

Episode 10 - Memorable Irina Quotes
"I need you to understand. I was eighteen when the KGB recruited me. For a woman to be asked to serve her country... it was a future. It meant empowerment... independence. I was a fool to think that any ideology could come before my daughter."
Irina: "How are your wounds healing?"
Jack: "You obviously had the chance to betray us in Kashmir, but you didn't."
Irina: "I don't imagine that means you decided to trust me?"
Jack: "Our previous... dealings... would indicate that your strategy here may be long-term, so for now, I trust that your behavior is predictable."
Irina: "By previous dealings, you mean our marriage. You know, technically... we may still be husband and wife. I'm sorry."
Jack: "Sydney's on assignment with Sark. It's my belief that he's still working for you... that you've coordinated your efforts to infiltrate both SD-6 and the CIA. Whatever you have in mind... I promise you... it won't work. So, I'm going to offer you a deal. I'll see to it that you're relocated to a private residence on Puget Sound... under twenty-four hour surveillance of course, but the illusion of freedom is better than none at all."
Irina: "In exchange?"
Jack: "In exchange, you'll confess... tell us what you're really doing here... why you've turned yourself in. I'll give you time to consider my offer."
Jack: "Have you thought about my offer?"
Irina: "I have nothing to confess, Jack. I know you find it hard to believe I'd turn myself in to make up for my mistakes, but that's the reason... the only reason... I'm here."
Jack: "If that's the truth, why didn't you simply refuse the offer?"
Irina: "I was considering whether or not to fabricate a confession, just to get out of this cell."
Jack: "You were right. Although our marital contract was founded on fraudulent pretenses, it's still valid until it's annulled. Which means, technically, we are still married."
Irina: "Jack... thus far, I've agreed to be debriefed only by Sydney. From now on, I'm willing to talk to you too."

Episode 11 - A Higher Echelon
As the episode opens, Sydney is at home talking to Will and explaining the nature of Echelon: a computer that can be programmed to recognize keywords. The government uses it to scan millions of communications each day looking for threats to national security. Her last mission recovered an access terminal that had fallen into the wrong hands. Also, a colleague of hers had been extracted out of SD-6 and taken into protective custody by the CIA. She expresses relief that the good guy's won again and that her friend is safe. The scene cuts to Marshall, her friend, who is being held by the man they'd retrieved the Echelon software from in London. He is being tortured to tell where the data had been sent. Upon threatening the life of his family, Marshall agrees to rewrite the program for them.
At the JTF, Kendall, Jack and Vaughn inform Sydney that the CIA had not intercepted Marshall as plan, and that they believed Cuvee and his men had abducted him. The CIA was searching for him as quickly as possible, because they knew he was in danger, and could also be coerced into re-writing the program for Cuvee. Jack tells her that Marshall had e-mailed the software to SD-6 before he was taken. He'd broken the program into several data packets, but one had been lost coming through a server in Vietnam. Sloane is tasking Sydney and Dixon to go to Vietnam and retrieve this data so that they can recompile the program.
Jack goes on to explain that in addition to the software, an access point, or "back door" into the system is needed. Without it, no one can access the system, even with the software. The CIA had analyzed the network, but had been unable to locate this access point. He tells her Irina thinks Cuvee might have used the Russian network to get into the system. Irina thinks she can find the overlapping access point, but she wanted unrestricted access to the Echelon network... a request Kendall refuses, as it is outside the parameters of her pardon agreement. Sydney's assigned counter mission will be to download the data packet, and provide Sloane with a corrupt data file upon returning to SD-6. Vaughn promises that the CIA will continue in their search for Marshall.
Meanwhile, Jack has problems of his own. Due to the murder of Emily Sloane and the successful extortion attempt against the Alliance, the head of Alliance Counter Intelligence has been sent into SD-6 to investigate. The woman, Ariana Kane, had originally started her investigation with Jack in order to quickly eliminate him as a suspect and then have him assist her. However, upon looking into his activities in depth, she realizes that he's hiding something, and assumes he is responsible for Emily's death. Jack enters his office to discover her downgrading his network privileges, and realizes how seriously she is looking into his dealings, so he rushes back to the JTF and has everyone assist him with fabricating hard evidence to support the paper records he'd created.
In Vietnam, Sydney and Dixon move in to recover the missing data packet, but Sydney runs into a problem when the hard drive is not in the server room as they'd thought. It had been sent in for repairs, and she races against Dixon to get there first to download the files. Dixon beats her to it, and she is unable to prevent SD-6 from getting what they need to recompile the Echelon system.
Back in Los Angeles, Sloane is overjoyed at their success. In a debriefing with Vaughn, Sydney expresses her disappointment at their failure, and also her disgust over Sloane's feigned concern for Marshall. Vaughn tells her that the CIA had traced Marshall to a safe house in London, but by the time the team arrived there, everyone was gone. He goes on to say that the location had been booby-trapped, and the entire team had been killed. Due to the tragedy, the CIA has halted their search for Marshall, and that he's on his own for the time being.
The CIA has been unsuccessful in its efforts to find a "back-door" point of access to Echelon within the Russian network. Desperate to find it and shut it down, especially in light of the fact that Marshall is most likely re-writing the program for Cuvee and knowing Sloane has all he needs to gain access, Kendall finally agrees to let Irina try to locate it for them.
While Marshall is being held at gunpoint, he manages to signal the SD-6 network over the internet. Dixon figures out that Marshall is the one trying to contact them and traces to IP address to a location in Mexico City. He enlists Sydney's help and they inform Sloane that they will lead the operation to rescue Marshall. They successfully rescue him and return to Los Angeles.
In the meantime, Kane has closed in on Jack, her suspicions growing after discovering brain matter on a revolver he'd checked out on the day of Emily's murder. She calls a meeting, and with the help of the CIA, he manages to avoid being taken into her custody. It is revealed that he had murdered a CIA agent the previous year that had been employed by Irina. His running from Kane cements his status as a fugitive from the Alliance.
Irina finally locates the overlapping access point, in spite of Kendall hovering over her shoulder. They confirm the connection and lock it down, just as Sloane celebrates gaining full access to the system.
The episode closes with Jack visiting Sloane in his home and telling him that he's innocent and needs his help tracking down a few leads. Sloane promises to help.

Episode 11 - Memorable Irina Quotes
Irina: "If you want to know where Cuvee breached the system, it'll take time. But I could do it if I were given access to Echelon. No restrictions."
Jack: "Kendall will never give that to you."
Irina: "Then I would simply ask you to inform Mr. Kendall that the technicians he'll assign to do the job will discover it is like quicksand."
Sydney: "They found it... quicksand."
Irina: "I told your father my terms... full access to the network... no restrictions."
Sydney: "Dad fought for you on this. Don't make him regret it."
Irina: "I'll need to send an access code."
Kendall: "How will we know you're not signaling your organization?"
Irina: "You won't."

Episode 12 - The Getaway
Jack is on the run from the Alliance due to Kane's investigation. He goes to meet a contact of his to assist him in proving his innocence, only to find that contact has been murdered. He narrowly escapes being taken into custody by Kane's agents, and is able to get away with Sydney's help. Kendall had called her in when Jack failed to report in the previous night. She takes him back to the JTF where he explains why Kane is there investigating. Sloane had revealed to him that the Alliance had ordered him to kill Emily because she'd learned of his involvement with SD-6. He thought he'd done so, but shortly after her funeral, he began receiving odd messages suggesting that Emily was still alive. Finally, the kidnapper had offered concrete proof Emily was alive and demanded one hundred million dollars in exchange for her safe return. The Alliance had paid the ransom in order to learn the identity of the kidnapper and assassinate him; only he'd gotten away with the money and had killed Emily anyway. He tells Syd that he'd no more been a suspect than anyone else, but because of his work for the CIA, his behavior and activities had raised questions, making him a prime suspect.
Sydney is angry that he'd not told her about this sooner and wants to help him prove his innocence. Jack forces her to return to SD-6 to prevent her from also being a suspect. In a debriefing with Vaughn regarding her latest mission for Sloane, Sydney learns that Vaughn has also been aware of the investigation into Jack's activities, and she is furious that he'd not told her anything.
Sloane has tasked she and Dixon with going to Nice, France, to recover a gyroscope missile guidance system that had been developed by the Triad. The CIA decides to send a team to follow her and duplicate the device on-site, so that a counterfeit gyroscope can be handed over to Sloane. She successfully steals the device from the Triad courier and hands it over to the CIA. Because it will take time to duplicate, Vaughn asks her to go to dinner, and they go... unaware that Sydney is under surveillance by Kane's agents. They discover Vaughn is actually CIA and move in to taken them into custody. Vaughn and Sydney manage to fight them off and kill them, but realize that their mission has been compromised and they'll be forced to hand the real device over to Sloane.
Meanwhile, Jack has received a secure message from Sloane informing him that none of his suspected leads had panned out. Sloane provides one of his own... Jean Briault... an Alliance member that he'd murdered the year before. He suggests Jack look into this further, as someone was most likely seeking revenge for that act. Jack takes the information to Irina and asks for her assistance in reviewing the records they have and brainstorming for possible answers. She agrees and after treating her to some Chinese takeout in her cell, she helps him find a few solid leads into who might be behind the extortion. Following them further, he discovers that Ariana Kane had been having an affair with Briault and had also deposited one hundred million dollars in an account the day the Alliance had paid the ransom. He goes to SD-6 to verify this information and is taken into custody by Kane's men. She plans to transport both he and Sydney to London for full interrogation, but while they wait for Sydney to return from her mission, Kane has Jack drugged with a truth serum, intending to begin her interrogation there.
Just before Jack reveals anything regarding his or Sydney's status as double agents, Sloane intervenes, having received a message Jack had sent to him concerning Kane's involvement just before he was taken prisoner. Sloane frees him and takes Kane into custody. Jack returns to the JTF and goes to see Irina to thank her for her help and tell her how everything had turned out. Both express a curious suspicion over the way things have turned out and wonder if there might be more to the story.
Sydney and Vaughn meet to discuss what their options are in light of their mission failure. Sydney reveals that she'd taken both devices with her when she left France, and due to the confusion surrounding the Kane investigation, she'd gone ahead and given the counterfeit gyroscope to SD-6. She hands the real device over to Vaughn to take back to the CIA.
We next see Sloane meeting with a man he had hired some months before to scramble the signal from the tracker the Alliance had inserted into his neck when he had become a full partner. He takes the device and kills the man, escaping the United States undetected by the Alliance. The episode ends with his arrival in Philippines at a house on the beach. In a shocking ending, he is reunited with Emily, who is most certainly not dead, thus revealing that he had in fact been behind the ruse to extort money from the Alliance and fake Emily's death, allowing them to escape for good.

Episode 12 - Memorable Irina Quotes
Irina: "Then if you're not here to say goodbye, why do you bring this to me?"
Jack: "I need someone to brainstorm with."
Irina: "Surely the CIA has teams that specialize in these matters... forensics... profilers..."
Jack: "Yes... they do."
"When I was your wife, I would meet my case officer in his hotel room. I suggest you find out where Briault stayed and pull the hotel security footage."

Episode 13 - Phase One
Kendall summons Sydney to the JTF for a meeting. Before the meeting, Vaughn pulls her aside and tells her that he can't go on much longer pretending that they don't have feelings for one another. Both agree that something must change. Weiss interrupts and reminds them about the meeting. They go in, and Kendall informs them that Arvin has been AWOL from the Alliance for five days, and that the Alliance is sending in a replacement, Anthony Geiger. With Sloane gone, Jack and Sydney no longer have the inside track into the administration of SD-6, so Kendall assigns them to get back into the "inner circle" as soon as possible.
Sydney reports to SD-6 and introduces herself to Geiger, who immediately begins questioning her about Danny and his death. He doesn't really understand how she could have returned to a job where her employer had murdered her fiancé. She explains that she had known she was breaking the rules when she told Danny about her affiliation with SD-6 and that she took responsibility for what happened. She'd returned because she was a faithful officer of the agency.
Leaving Geiger's office, she runs into Sark, who expresses concern over the new arrangements. Sark mentions that Geiger had bragged about unlocking Sloane's secret files on Server 47. Sydney is puzzled, because there were only forty-six known servers in the SD-6 network. She takes the information to the CIA, and upon further investigation, they learn that Server 47 is actually an airplane belonging to the Alliance that housed their main computer system. They'd never have located it, because it was constantly moving. The Alliance paid a man to travel with the plane, compensating him with paid companions on a regular basis. The CIA inserts Sydney onto the plane as one of those companions, and she renders the man unconscious, hacks into the server and transmits the data to Vaughn and Weiss who are traveling in another plane within five thousand feet. As she is disabling the remaining guards, a gunfight breaks out, and she shoots out a window of the plane, barely managing to grab a parachute on her way out the door.
The CIA analyzes the data recovered from the server, and realizes that they have what they need to take down the Alliance, if they can verify a code within the document. Jack volunteers to go to SD-6 and get the code from their computer system, unaware that Geiger has learned that he and Sydney are double agents. He's taken into custody, and Geiger orders him to call Sydney in... he does, but gives her a signal they'd devised the previous year to alert the other if one of them was discovered. Frantic, Sydney realizes that they must do something quickly to verify the information in the document in order to take down SD-6 and save her father. She goes to Dixon and tells him the truth about SD-6... that it's Alliance, not CIA... and she begs for his help in acquiring the code. Hurt and angry, he nevertheless acquires the code and emails it to Sydney.
The CIA, in conjunction with various intelligence agencies worldwide, takes down SD-6 and all other Alliance assets. Sydney races to save Jack, and kills Geiger in the process. She tries to thank Dixon after it's over, but he tells her not to speak to him again. Standing in the rubble, Sydney and Vaughn realize it's finally over, and they rush into one another's arm for the long awaited first kiss.
Sark phones Sloane to let him know that Phase 1 was complete - Sydney had leaked the information about Server 47 to the CIA as Sloane had predicted and the Alliance was no more. Sloane instructs Sark to move on to Phase 2, and orders that he check in with their Los Angeles asset. The final scene cuts to Francie's restaurant and her receipt of Sark's phone call verifying she is in place. She confirms, and we see that it's not Francie at all, but a double who looks exactly like her. The real Francie has been murdered and is lying on the floor in her restaurant's kitchen.

Episode 13 - Memorable Irina Quotes
None for this episode

Episode 14 - Double Agent
In Berlin, a young CIA agent named Emma Wallace realizes that her partner, Jim Lennox, is not who he seems. She attempts to contact the CIA, but he renders her unconscious. He phones his associate, Arvin Sloane, to inform him that he's been compromised. Sloane orders him to murder Wallace in a public way, sending a message to the CIA. He straps Wallace down with C-4 and dumps her out on a busy Berlin street corner.
The agents in the JTF watch in horror as she is murdered. Kendall explains that Wallace and Lennox had been on an undercover assignment to gain information on one Dr. Renzo Marcovic, in order to learn more about a project he'd been developing called Project Helix. Lennox' last known communication had been traced to a facility in Cayo Concha, so Kendall sends Vaughn and Sydney there to rescue him and download any information on Project Helix they could find and bring it back to the CIA for analysis.
They are successful, and upon returning to Los Angeles, they learn that Project Helix dealt with next generation molecular gene therapy, allowing for a person's genetic code to be altered, so that they could take on the appearance of someone else. They discover that the first recipient of the process was Dr. Marcovic, who had taken on Lennox' appearance. The team's investigation into Wallace's murder leads them to video footage of the man who detonated the C-4... he appears to be Lennox. Not knowing if the Lennox they have in hiding is really their agent or Dr. Marcovic, the CIA takes Lennox into custody and administers an ocular scan in order to learn his true identity. He's cleared.
The team learns that the doctor had moved the Helix prototype from Cayo Concha to a freight yard in Poland, so Sydney and Lennox go to Poland to download the schematics and destroy the prototype. While they are there, the JTF receives a call from a man who claims to be the real Agent Lennox. He claims the ocular scan was false data that the doctor had included in the data to throw them off-track. He's in Poland and headed for the freight yard. Jack orders Sydney to take both men into custody and they'd sort it out upon her return to Los Angeles. This plan goes awry and ends in a standoff between the doctor, Lennox and Sydney. She realizes the only way to ferret out the imposter is to destroy his only chance of getting his own face back someday... by blowing up the prototype. She detonates the explosives she'd rigged earlier, and Lennox shoots Marcovic as he attempts to kill Sydney. The man who'd been with Sydney all along was the real Jim Lennox. Additionally, they learn that the prototype had been used at least once before, meaning someone else had been doubled, but they don't know the identity of that person. They return to Los Angeles, and Lennox bids farewell, and goes on vacation in order to get over Wallace's death.
Sydney cooks dinner for Vaughn, and they finally consummate their relationship, unaware that "Francie" has bugged the apartment and is watching them from the video camera hidden in Sydney's bedroom.

Episode 14 - Memorable Irina Quotes
None for this episode