The confrontation was triggered by the Agency, which assaulted Phagan's warehouses in Almaty, Kazakhstan, following Rhoemer's attempt to launch a missile at a classified target, which failed thanks to Gabe Logan, who threw a wrench into the man's endgame and killed him. Specifically, it was masterminded by Dillon Morgan and Derrek Falkan, who rendered Xing unconscious and captured a CDBC member Dobson alive. However, they failed to extract the prisoner's plasma, for she recovered quickly and proceeded to flee the base. Struggling from internal strife, the Agency members began to turn on themselves, initially arguing over the faults certain people carried, before later quarreling about the fate of Phagan. As such, they suffered from substantial casualties, including Mr Cochran who Mara Aramov killed for failing to complete his duty, and Jonathan Phagan, whose life support was switched off by Dillon Morgan to eradicate any incriminating evidence of Syphon Filter contaminating the PHARCOM CEO.
Following the Kazakhstan Missile Incident, Gabriel Logan and Lian Xing along with the CBDC investigate the Missile Silo that Erich Rhoemer fired a nuclear missile from. In the surrounding Pharcom Warehouses they recover Pharcom data and personal files from Jonathan Phagan placed onto Data Discs, which could help them discover a cure for the Syphon Filter Virus that Lian is currently infected with.
The Agency, aware of the Black Baton attack on the warehouses and Logan's presence there, arrive in two Black Hawk Helicopters led by Dillon Morgan and Derrek Falkan, with Steven Archer piloting one of them. With them is several teams of Spooks with the mission of eliminating Logan and capturing Lian Xing along with the Data Discs, to prevent that data from landing in the SVR's hands. They manage to capture Lian (as well as a CBDC agent by the name of Dobson) while evading Gabriel Logan in the process. Dr. Elsa Weissinger confirms that Lian is a match for being infected with the virus and Morgan orders a retreat, heading towards the McKenzie Airbase with her in tow before the Russians arrive. Gabe kills some Spooks and rushes to rescue Lian but is too late.
With Steven Archer tasked with hunting down Logan and the Data Discs, the remainder arrive at the airbase where Lian and Dobson are taken in under the moniker as "terrorists" so that the Military Airmen don't become suspicious. The airbase itself is currently used to smuggle (in secret) Syphon Filter Virus infected Corpses to avoid security checks and customs, under the guise of "FEMA".
The Agency's infighting
Cochran: W-We're working on it now. You'll have your shipment by the end of the week.
(Unknown Man on phone) You have three days! If I don't have it by then, there may be a leak to the American press.
Cochran: I'm sorry, but (click)
Mystery Man (in room): Most unfortunate.
Cochran: Stevens' men have the woman now. As soon as they get the plasma-
Aramov: What about Logan?
Stevens: There wasn't time. The U.N. peacekeeping forces had already arrived.
Aramov: Another Agency screw up! Do you have any idea how close your incompetence has come to killing us all?
Stevens: I am not responsible for the actions of my predecessor. Markinson was not in control.
Aramov: Markinson was your man!
Stevens: As Rhoemer was yours. And what about Gregorov? You were supposed to keep the Russians away from the Pharcom warehouses at Kazakhstan.
Aramov: You're not going to blame me for your incompetence! The SVR is not under my control any more than Rhoemer's terrorists were!
Mystery Man: Enough. We all have much at stake.
Stevens: Logan was one of our best agents. He has the highest level of training and years of field experience. It won't be easy.
Mystery Man: I see. Perhaps I'm not being clear. Success is everything. Is it not, Mr. Cochran?
Cochran: It will be impossible to get the plasma from the woman as long as Logan is still alive!
Mystery Man: I think you overestimate Mr. Logan's abilities. You were given Mr. Phagan's job because you promised to have Phase Two of the virus ready in time.
Cochran: It's not my fault that Rhoemer lost the girl before we could extract the-
Mystery Man: But like Markinson and Rhoemer, you have failed.
Cochran: All right look, I'm sorry that things didn't go according to plan, but-
(Aramov reaches over and snaps Cochran’s neck with a vicious twist.)
Mystery Man: You see, Mr. Stevens? A simple demonstration. Mara has proven her usefulness, Mr. Cochran has not. Logan will be taken care of. We will have the female's plasma soon.
Stevens: I have an army on the way to Colorado now, and my men are at the airbase with Lian Xing.
Mystery Man: There will be no more delays.
In Washington D.C., a secret council is being held between Agency members, chiefly Lyle Stevens, Mara Aramov, Mr. Cochran and a shadowy man. Shi-Hao, a Chinese General seeking to force war with the Russians, is heard on the phone speaking to the group warning them that if he doesn't get his shipment soon there may be a "leak to the American Press". After hanging up the phone, the shadowed man simply comments on how unfortunate that call was before Mara and Stevens argue among one another for Erich Rhoemer's actions.
Aramov questions if Gabriel Logan has been dealt with and Stevens replies that the UN Peace Keepers had arrived not giving his men enough time. Mara concludes that this is another Agency screw-up and that their incompetence has been bringing them closer and closer to killing all everyone. Stevens retorts that Thomas Markinson as his predecessor wasn't in control while Mara responds that he was Stevens' man. He counters this by stating that Rhoemer was hers and addresses the topic of Uri Gregorov whom she was supposed to keep away from the area. She scoffs at the suggestion, protesting that the SVR wasn't under her control just like the Black Baton under Rhoemer.
The shadowy man interposes, stating that's enough and adds they all have much at stake. Stevens continues insisting that Logan was their best operative with years of experience that would not make this easy, something that the shadowed man idly comments on. He says that perhaps they didn't understand what he was saying, that success is everything and directs his speech towards Mr. Cochran who begins making excuse after excuse involving the delays in getting plasma from Lian Xing. It's revealed that he was given Phagan's job as he promised to have Stage Two of the Syphon Filter Virus ready on time but it has become obvious that Cochran has failed, as Rhoemer and Markinson before him. While Cochran tries one last time to reason for his actions, Aramov impatiently snaps his neck and he falls dead to the floor while the shadowy man explains how Mara has proven her usefulness where Cochran has not.
He goes on to state that Logan will be taken care of and the girl's plasma will be ready on time. Stevens tells him that he has an army on the way to Colorado and Xing is already in route to the airbase.
Arrival of 'FEMA'
Morgan: You can take a break, airman. We'll be done in ten minutes.
Airman: I'll need to see your I.D. sir.
Falkan: We're with FEMA. Do we need to refer to your commander?
Airman: Uh, no sir.
(The airman leaves, slightly curious about them)
Morgan: We'll check on Phagan. You finish the other CDBC agent. Stevens wants us back in New York.
Dr. Weissinger: Watch her. She's been unconscious for much longer that I would have expected. The virus should not have weakened her so much this early in its development cycle.
Holman: I'll head over to the secured hangar and see if the F-22s are back for refueling and ordinance.
Morgan: No. You get over to the main gate and make sure our package gets through unhindered. I'll take care of the pilots personally.
Dillon Morgan arrives outside of Lian's room with Dr. Elsa Weissinger and an Unnamed Agency Doctor. An Unnamed Airman asks for their ID before Thomas Holman announces him and the rest as "FEMA" while also threatening to inform the airman's superior. He apologizes and leaves while Weissinger enters the room with the doctor, telling him to be careful as she expresses her concern that the virus has weakened her this quickly in the development cycle. She proceeds towards Dobson's room while Morgan heads to Jonathan Phagan's room and Thomas Holman goes to check on their shipment. Falkan suggests heading over to the F22's himself, but Morgan says he'll "deal with them personally".
Meanwhile, inside the room with the doctor, he says that two bags of plasma should be enough while stating she shouldn't feel a thing. Lian suddenly punches him in the face and he falls unconscious beside the bed, while she replies that "he's the one who won't feel a thing" while weakly standing up.
Staving off Syphon Filter
Lian Xing is weakened due to the effects of the Syphon Filter Virus and needs to find an adrenaline shot. She sneaks out of her room and makes her way through the hallways avoiding Airmen until she comes across Derrek Falkan outside of a room that Dr. Elsa Weissinger exits. He asks if she's finished with "him", to where she replies that she gave him the shot and it will take a moment to go into effect. She wishes to check on Xing, however Falkan says she needs to go to Phagan's room right away. The two walk by and Lian makes her way into the room they were just in to take the shot. She looks on the bed to see Dobson and morns, asking why he didn't stay back when she told him to. She bids farewell to him and continues on further into the complex.
Elsa Weissenger and Dillon Morgan's argument over Jonathan Phagan
Falkan: I've relieved the guard. We won't be disturbed.
Morgan: Good. Doctor, is your work with him done?
Dr. Weissinger: Yes, that's the last we need from him. We get the rest from Xing.
Morgan: Then let's tie up a loose end. Unplug him.
Dr. Weissinger: Wait! I can still use him back at the lab. We still have not fully studied the long-term effects of the virus on certain genetic structures. I can use him!
Morgan: My orders are to make Phagan disappear when you have finished extracting his plasma. The Agency can't risk the government finding Pharcom's CEO infected with an unknown virus.
Dr. Weissinger: I see. It doesn't help that he has Aramov's bullet in his brain, does it?
Morgan: You can use the girl for your other tests.
(Morgan personally cuts off the life support, and Phagan immediately dies)
Dr. Weissinger: Fine, if you insist. I'll call the New York labs and see if they're ready for us.
Morgan: I'll go with you. You go on ahead and check on the F-22s. Make sure they have the Sarin canisters loaded and ready for a run on the survivors.
Falkan: I'll see what's keeping Holman.
Lian comes through the observation end of a room where Jonathan Phagan was being kept in a comatose state. Weissinger finishes extracting the plasma from Phagan, while Dillon Morgan insists on removing his life support. Weissinger tries to claim that he could still prove useful at her lab but Morgan reveals that his orders are to eradicate incriminating evidence. He suggests they kill Phagan lest the Government find the Pharcom CEO rotting away in this room. He goes ahead and pulls the plug much to Weissinger's dismay, with everyone exiting the room shortly thereafter.
Recovering Lian's gear
Lian: Gabe? Are you there? Gabe?
Teresa: Lian, where are you? Are you all right?
Lian: Teresa? It's good to hear a familiar voice. I'm fine. They're holding me at some civil airbase in Colorado. Where's Gabe?
Teresa: He's run into trouble. Transport's down somewhere in the mountains.
Lian: Gabe's in trouble?
Teresa: Yeah, but what else is new? I think he's more worried about you than himself.
Lian: Gabe knows better than to worry about me.
Teresa: Lian, are you okay?
Lian: I'm running on an adrenaline booster right now. Winding down fast. Get this information to him right away. He was right about Phagan. They were keeping him alive incubating some new strain of the virus. Probably the same strain I'm infected with. They must've injected us both while we were imprisoned in the catacombs.
Teresa: Oh my God!
Lian: I'm sure that's why they brought me here. They were using this airbase to fly infected test subjects in and out of the states bypassing international quarantines.
Teresa: The Agency's also using it to shut down air routes all over the Rockies.
Lian: Makes for a good front. Tell Gabe that the Agency lab complex is somewhere in New York. I'm gonna try to find out where. Okay, (coughs) I'm gonna get a chopper and I'm gonna get out of here. Does Gabe have an EVAC plan yet?
Teresa: No, he's having me monitor Agency radio traffic while he gets to the crash site. I think he's gonna try to requisition a chopper there.
Lian: Tell him not to, I'll give him a ride myself. Do you have his coordinates?
(Morgan and the female arrive at the gate)
Morgan: We're ready to leave airman. Buzz us out.
Carter: Yes sir.
Lian: Never mind, I'll get them from the tower.
Dr. Weissinger: I'm going to head over to the other infirmary and make sure that the rest of the plasma has been properly refrigerated.
Morgan: Okay, our F-22s are coming in now. As soon as I deal with them I'll meet you at the tower.
Lian enters the room, taking a glance at Phagan before heading to a Restricted Area (where her Combat Gear is being kept). She notices an Unnamed Airman talking to Carter at the reception desk, saying he needs to get some fresh air with these government types looming about. He grows even more untrustworthy when he learns about several body bags being brought in and the place having been locked down tight. Carter buzzes him through and he moves into the lower level, while Lian sneaks under the window and into the back where she obtains her gear.
The truth revealed
Airman: All right hold it, Miss. Stop right there.
Lian: You don't understand. I'm not a prisoner. You don't know who these men are.
Airman: You're right. I don't know who they are, but I know they're not from FEMA, over here. I overheard two of them. They're planning to kill you. You can get out here.
Airman: If you're trying to get to the airfield, it's southwest of here. I'll check in at the security office and cover your absence as long as I can. Good luck.
Lian: You're taking a huge risk, airman.
Airman: I took an oath to uphold the law. Who are these people? CIA? NSA?
Lian: Not exactly.
Airman: You don't have much time. Good luck.
Lian: Thanks again.
After zapping Carter with her hand taser, Lian leaves and incapacitates a second patrol. She finds a door to the inner perimeter, where an armed airman tells her to surrender. She tells him the truth: he doesn't know who the 'FEMA' men are, and he replies they're attempting to kill her. He lets her out, telling her where the airfield is, and he will cover her absence for as long as possible.
Morgan's plan to bomb the mountain
Morgan: Commander, Stevens wants me to personally thank you for the job you've done here.
(He pulls out a silenced pistol.)
Pilot #1: W-Wait a minute!
(Morgan casually fires once into the pilot’s forehead.)
Morgan: Now Commander, we will try again. Get this plane refueled. We have another mission for you to fly. No one gets off that mountain alive.
Pilot #2: Yes sir!
(At the entrance to the outer perimeter)
Lian: Teresa, come in. I'm out of the holding complex.
Teresa: I read you. What's your plan?
Lian: First, I'm gonna find a decent silenced weapon in case I run into any Agency operatives. Then I'll have to find some way to get into that air traffic control tower.
Teresa: After all that, finding a chopper to hitch a ride on should be a piece of cake. How you holding up?
Lian: I've been better. Out.
Sergeant: Vallery, one of the feds needs a lift over the main gate. I want you to double-time it over to Admin and drive the truck for him.
Vallery: Who are these guys, Sarge? What the hell are they up to?
Sergeant: Don't ask questions, airman. Just move.
Vallery: Yes, sir.
In the hangar, Morgan approaches a pilot to 'thank him', and kills him with a pistol. He then tells a second man they have a mission and nobody can get off the mountain alive. Lian intends to acquire a silenced weapon and access the air traffic control tower.
Lian's plan to interrogate Holman
Lian: Teresa, I've got something. I think I just saw Thomas Holman here at the base. We went through Agency training together.
Teresa: Holman… Don't know him.
Lian: He was assigned to the FEMA unit. I'm betting he'll know where the labs are.
Teresa: So what are you gonna do?
Lian: I'm gonna get him to tell me.
Sabotaging the F-22
You'll start the mission off behind two soldiers talking. Listen to them, as you sneak up to a bush nearby. Hide there until one of them leaves, and then sneak up on the other dude, and taser him.
Run in the direction that the other guy ran in, and after you round two corners, you'll get a cutscene. Now flatten yourself on the wall to the left, and wait until the soldier patrolling near the truck turns around. After he has, run forward, and as you get closer, sneak and use your taser on him. Pick up the Sniper Rifle from the back of the truck.
There's a guard to your left now. Sneak up to him and taser him, if you can't seem to get him, try running in a big arc to get him. After tasering him, go into the alley and climb up the wall. Drop onto the truck and hide around the corner.
The soldiers will say something like, "Hey, did you hear that?" Climb up the green boxes, drop over the other side (quietly!), and taser the guard from behind. Leave him and continue in the other direction.
Around this corner, you'll hear Morgan and Falkan talking. Hide behind the corner/box, as a soldier will head your way. Taser him, then follow Morgan and Falkan outside again. Take a right, flick the switch, and the roller door will open for you. Equip the Silenced Sniper Rifle, and sneak up to the guy on top, nail him with a head shot. Now head to the underside of the plane, and press Triangle to sabotage it.
Equip the Hand Taser now, and hide behind a corner, as a soldier will be coming your way. Zap him, and return outside. From where you are, crouch and take a right. Get around here, avoiding the soldiers, and move forward. Watch the searchlight, and then cross when it's safe.
Interrogating Thomas Holman
You'll get a checkpoint, move to the top-left hand corner. A truck will drive by soon, jump on to it, and once you see an opening to your left, jump off and quickly run to it.
Once you've jumped off, head into the hangar there. Make your way over to the exit, and you'll get a cutscene. Now you have to extract information off Holman. From the alleyway that you're in, take a right, back into the hangar. Go around the other side of the truck, and wait until the two dudes start talking. Sneak up to them, and once Morgan shoos the soldier away, taser the soldier. Follow Morgan quietly into the hallway, and you'll get an FMV.
Finding the transponder frequency
You'll receive a HK-5. Head back, and creep up on the guard near the green crates and taser him. Now, this is where you'll need to be careful. Equip the Silenced Sniper Rifle, and run into the corridor to your right. Look up, and there's a searchlight. Snipe it out.
Run back down the corridor, and equip the Hand Taser. Run out, and follow the guard around and tase him. Run to the fence, and make your way to the truck. Go up to the door, and ignite it. The truck will reverse and crash into a building; the soldiers will be like, "WTF?" and that's the diversion that you needed.
Go into the building, and take a right into the elevator. Go up, and once you're out, take a right, and go around. Be careful, around the second corner is a soldier, taser him. Sneak up and taser the guy who's talking. Find the Transponder Frequency on the wall, and now leave via the elevator.
Stealing Falkan's copter
Take the left path this time, and you'll reach the outside, where Morgan and a soldier are speaking. Falkan will head to the chopper, and you'll follow. Sneak up and tase the guard, then tase Falkan. Run to the chopper, and that's it!