During his mission, Logan was ordered to administer an apparent antidote to test subjects who were infected with the Syphon Filter virus. It was only later that Lian Xing figured out it was not supposed to cure them, since there was no universal cure, and events were engineered such that Gabe was in fact killing them with a lethal chemical. Nonetheless, he was largely successful, rescuing a now infected Lian and being brought to the PHARCOM warehouses due to Mara Aramov's desire to stop Rhoemer from launching a missile. Black Baton forces in Rhoemer's stronghold were presumably killed or they simply disintegrated.
"My God... Syphon Filter!"
"Yes, it's quite remarkable. A virus genetically programmable to eliminate anyone or anything... Imagine a weapon that could target specific demographics, ethnic groups... it could wipe out whole continents, except for those chosen to survive."
"The outbreaks we've been tracking..."
"Tests, evidently... We've traced Phagan to this abandoned cathedral. According to Mara, this is Rhoemer's stronghold. A place where he keeps prisoners. Undesirables. Alec Kabanov runs the site for Rhoemer. He kept Phagan supplied with human test subjects for various forms of the virus. Now Phagan is being held prisoner himself, probably somewhere in the catacombs."
"Has Interpol found any trace of Mara?"
"Since her escape, she's left a trail of bodies from our lab to Eastern Europe. Now she's vanished. There is also no sign of Rhoemer. The destruction of his base has driven his entire organisation underground. We've found and destroyed all PHARCOM labs involved in the production of the virus, but we cannot find the computers they were using for the viral DNA sequencing. You have to get their location from Phagan. Your team-"
"I don't want a replacement for Lian."
"You don't get one. I'll be taking you into the strike zone myself. Our labs have been able to synthesise a very small amount of vaccine. Give one shot to any test subjects you find. Radio me as soon as you find Phagan. One more thing. You are directed to eliminate any of Rhoemer's medical personnel that get in the way."
"Copy. I'll let you know when I've found my way down to the ground level."
With Rhoemer's base destroyed, Black Baton is driven underground and Mara Aramov goes missing. Markinson briefs Gabe on Syphon Filter, a virus that can target specific genotypes, leaving certain people alive while killing only its victims. He then mentions Phagan's presence in a cathedral occupied by Rhoemer's forces, and tells Gabe to contact him when the PHARCOM founder is located. He also tasks Logan with injecting test subjects with a vaccine which the labs developed.
Administering the vaccine
When Gabe infiltrates the compound, he locates numerous guinea pigs who have been infected with the virus and issues the antidote to them. He also goes about terminating the scientists who interfere with his tasks.
Finding security cards
In the course of his mission, Logan encounters a couple of opposing forces who possess a security keycard. He neutralises the threats and pockets the required items.
Going into the lower levels
"I'm finding PHARCOM and WHO shipping containers everywhere. Rhoemer and Phagan must've been working on something big."
"Stay focused on the mission. Don't get distracted."
Riding an elevator down to the bottom, Gabe resumes his various tasks. He eventually arrives at the catacomb entrance.
Search for Phagan
"Security has been breached. Rhoemer has ordered that the prisoners be eliminated. Take care of the old man. I'll wait here."
"All of Rhoemer's underground security is palm-print activated. You must follow the guard and let him open the cell. If you're seen, you won't be able to get in."
"Have an evac standing by. It won't be long."
Gabe encounters a guard who tells a scientist to terminate the 'old man'. By stealth and guile, he shadows the medical staff to Phagan's cell while dodging armed personnel who he comes across.
Escorting Phagan to safety
"Please! Don't kill me!"
"Just relax. This won't hurt a bit."
"I'll PAY you! How much d'you want?! Thank God!"
"Shut up Phagan! Move! I have him."
"Give him 30 seconds to give you the location of the computers. Then eliminate him."
"No, wait a minute! You don't understand..."
"Thousands of people are dead, Phagan, because of you! Twenty seconds..."
"Wait, you don't understand..."
"Time's up! Where're the sequencing computers?"
"An abandoned Soviet missile silo in Kazakhstan. Beneath an old warehouse district. Alright? Alright?"
"Did you copy that?"
"Copy. I've got a strike force ready to move in. Get to the evac point. I'm sending in a retrieval unit."
"What about Phagan?"
"Take him with you."
"Wait... Let me go... Your partner... She's alive!"
"Lian? You're lying... Move!"
"She is alive. Rhoemer's men brought her here five days ago."
"I don't believe you."
"Promise to let me go, and I'll lead you to her."
As the scientist arrives at Phagan's cell, the PHARCOM CEO tries in vain to talk the man out of killing him. Suddenly, a shot is fired at the white-coated worker and he drops dead. Gabe enters from behind and orders Phagan at gunpoint to tell him where the sequencing computers are found. Phagan submits to him, claiming they're in Kazakhstan. He follows Gabe to the evac point, but then claims to have seen Lian alive. Gabe is initially skeptical, but then decides to let Phagan show him where his partner is.
Escorting Lian to safety
"That's her cell. You're on your own now."
"Gabe! How did you get here?"
"Thank God! I found-"
"We have to get out of here. The Syphon Filter virus is-"
"I know. We have the computer's location. Markinson's on his way."
"Gabe, I've been infected. We have to get to Phagan's warehouse before the Agency destroys everything."
"But they've found a vaccine. The test subjects-"
"There is NO universal vaccine! You have to know the specific genetic lock and key for each programmed virus! Only Phagan's computers have that information..."
"But that means..."
"Follow me. I know the way out."
With Gabe locating Lian, Phagan bugs out from the catacombs. Although initially optimistic, telling his partner they have the computer's location and that Markinson is coming, he eventually learns that Lian was infected and they must reach the PHARCOM warehouses before the Agency destroys the compound. He then argues with Lian, who counters that the virus does not have a vaccine. She knows where the exit is, and leads him there.
Attempted assassination of Phagan
"They're all the same in the end."
"We don't have much time. If we don't stop 'em, we'll all die. Come on, I have a chopper."
As they reach the exit, Gabe and Lian find Phagan pleading for his life, but he is shot anyway... the assassin being Mara, who tells them they're running out of time, and will all die if nobody acts. Since she has a helicopter, she can assist the duo in stopping Rhoemer.
With Gabe repeatedly sent in to their complexes, Black Baton forces are significantly dwindled. They later wind up fighting against PHARCOM security forces in the warehouses, where Gabe is dropped in to stop Rhoemer's agenda. Phagan, although braindead, is in fact still alive, and is transferred to MacKenzie Air Force Base where tests are run on him after he is hooked up to life support.