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
Meanwhile in Washington D.C., a secret meeting is being held between 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 mentions Thomas Markinson as his predecessor who wasn't in control while Mara claims that he was Stevens' man. He replies by stating that Rhoemer was hers and brings up Uri Gregorov whom she was supposed to keep away from the area. She scoffs at the suggestion, saying that the SVR wasn't under her control just like the Black Baton under Rhoemer.
The shadowed man says that's enough and states that they all have much at stake. Stevens goes on to say 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, like Rhoemer and Markinson before him. While Cochran tries one last time to save face, Aramov impatiently snaps his neck and he falls dead to the floor while the shadowed man explains how Mara has proven her usefulness.
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'
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
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 make Phagan disappear, lest the Government find Pharcoms CEO rotting away in this hospital room. He goes ahead and pulls the plug, with everyone exiting the room shortly thereafter.
Recovering Lian's gear
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
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!