A mysterious political and paramilitary organization (Most likely based on the Central Intelligence Agency), simply labeled as the Agency, was the first and perhaps most influential group standing behind the Syphon Filter conspiracy. Initially seated in Washington D.C., the Agency operated on a global scale, covertly and seemingly without any involvement in international affairs. Its true nature was revealed only later, showing that it is, in fact, a government funded arms consortium with the sole purpose of arming Black Baton, and Vince Hadden's front for controlling the circulation of the Syphon Filter virus and gaining power in the US and other world governments.
According to Gabriel Logan's testimony from the congressional record, the Agency made its first appearance in Afghanistan during the late eighties. Although their presence there was covered by Edward Benton who claimed to be a CIA agent transporting arms to the local rebels, Benton clearly stated afterwords that he was part of a US intelligence agency and recruited Logan and his demolitions expert Ellis as field agents shortly after they both left Afghanistan. It is unknown whether the munitions run made by Benton was actually a cover for an arms delivery intended to reach terrorists due to the lack of evidence.
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Paradise Ridge incident
Sometime in the nineties, a seemingly important Department of Defense satellite lost orbit and crashed in the wilderness of Paradise Ridge, Montana. It was apparent that the satellite, having recovered some sensitive data that could cause trouble if it had fallen in the wrong hands, fell prey to a local survivalist organization under Oakton's leadership called the Foundation to Inhibit State Treason. Teresa Lipan was sent by the Bureau of Alcohol, Tobacco, Firearms and Explosives to investigate a disturbance involving small arms violence, which actually proved to be a conflict between corrupt National Security Agency government operatives (claiming to be the Federal Bureau of Investigation seeking the satellite) and Oakton survivalists. Gabe Logan rescued Teresa before she could be executed, and she later led the Oaktons to safety.
Costa Rican incident
Some time later, Gabe Logan and Lian Xing were sent by Edward Benton to infiltrate Rhoemer's plantation in Costa Rica, where an undercover operative Ellis was inserted earlier. Alerted of the intruders, Rhoemer ordered that Mara Aramov shoot Ellis, and had Girdeaux incinerate all the incriminating evidence of his operation. The plantation workers were killed as well, and Rhoemer loaded his plane with crates that contained the extracts from plants he was growing.
Gabe was tasked with sabotaging Rhoemer's helicopter, transmitting the coordinates to headquarters so an airstrike could attack the plant, and acquiring samples of the plant. He then liberated a couple of slaves in the vicinity and decided to pursue a personal agenda of exacting revenge against Rhoemer, despite Benton's warnings that his actions 'would not go unpunished'. He drove a vehicle towards Rhoemer's plane and leaped aboard before it took off.
On the plane, Gabe decided to leave the pilot alive in order to keep everybody airborne. He encountered Rhoemer, the latter wearing heavy duty armour he would later find on Jason Chance, and used a USAS-12 to blast him backwards. The terrorist fell off the plane, only to escape and plot the Washington DC attack.
While Gabe was busy pursuing Rhoemer, Lian was told to recover samples of the plant materials that were being synthesised. She collected the data discs and destroyed all the computers; she was also instrumental in rescuing medical scientists who Rhoemer had captured.
Her mission complete, Lian then headed to the Australian outback, acting on information Gabe had recovered with Maggie Powers during an operation to scuttle the SS Lorelei. She took pictures of genocide as photographic evidence, sabotaged the compound's communications and acquired components essential to creating a Syphon Filter antidote, before catching Dr. Elsa Weissenger. She told the doctor to synthesise the vaccine, which she planned to use on Aborigines who the Agency used to test different strains of the virus.
Under heavy stealth, Lian took down Commander Silvers, who was in charge of the operation. She then administered the vaccine to the Aborigines and stole a truck which she drove to the landing zone. It was only when she got there that she discovered Dr. E had disappeared.
Washington DC attack
Rhoemer eventually initiated an assault on Washington, deploying multiple viral explosives. Gabe was sent into the area with CBDC, and he was tasked with throwing a wrench into the terrorist's plans. He took down many of Rhoemer's henchmen, including Pavel Kravitch, Jorge Marcos, Anton Girdeaux and innumerable waves of terrorists, before the crisis ended.
First PHARCOM investigation
Gabe's investigation takes him to a new lead from PharCom, a multinational pharmaceutical and biotechnology corporation headed by Jonathan Phagan. The Costa Rican plantation was growing PharCom compounds, meaning Phagan and Rhoemer were in cahoots. At the PharCom Exposition Center, Gabe shadows Phagan to a meeting with Aramov and Edward Benton, an apparent Agency turncoat who assisted Rhoemer during the Washington, D.C. attack.
After Gabe eliminates Benton, he saves Phagan from assassination only to have him escape. Mara Aramov, now in custody, had attempted to locate PharCom's virus labs.
Destruction of Rhoemer's base
Gabe must set aside the hunt for Phagan to destroy Rhoemer's base in Kazakhstan. During his assignment, Rhoemer seemingly kills Lian, but Agency Director Thomas Markinson rescues Gabe.
Sabotaging Rhoemer's stronghold
Markinson gives Gabe a report on the virus called Syphon Filter, a bioweapon that one can program on a genetic level to target specific groups of people. Markinson orders Gabe to infiltrate Rhoemer's stronghold in Ukraine to inject test subjects with a vaccine and locate Phagan, who is now Rhoemer's prisoner. In the catacombs, Phagan tells Gabe that Lian is alive, and they reunite. Lian has become infected with Syphon Filter, and she says there is no universal cure. Mara Aramov arrives to shoot Phagan, but she convinces Gabe and Lian that she came to help. They head to Pharcom's warehouses to stop Rhoemer from launching a missile.
Kazakhstan missile incident
The three travel to PharCom's warehouses in hopes of preventing Rhoemer from launching a missile. Lian reveals that the serum Gabe injected into the test subjects was really a lethal chemical, and Markinson was having them killed. Using the fighting between Rhoemer's terrorists and Phagan's guards to cover his insertion, Gabe descends into a silo and searches for the missile's detonation codes. He finds Markinson and gets him to confess that the Agency has been involved in the plot all along. Rhoemer worked for Markinson, since the latter wanted the virus in the Agency's possession. He never authorized the missile attack, but before he can stop it, Rhoemer kills Markinson with a headshot. Gabe must reach the missile's control center in time and destroy it. Enraged, Rhoemer engages Gabe in a final fight, but is killed with a gas grenade.
Their mission completed, Gabe and Lian call in the U.S. Army Chemical and Biological Defense Command (CBDC) to secure the area. They do not know how far Markinson was cooperating with Rhoemer and Phagan, but Gabe believes they may never know. In a post-credits scene, Aramov approaches a mysterious man inside the Agency headquarters and whispers something in his ear. He congratulates her while the camera pulls back to show PharCom boxes in the office.
The search for the data discs
This is a temporary list of individuals involved, more elaborate details will be added later.
- Vince Hadden: second-in-command and US Secretary of State; he attempts to blame Gabe and company for the terrorism that occurred on US soil during Syphon Filter and its sequel
- Thomas Markinson: Initial director
- Edward Benton:
- Lyle Stevens: Deputy director who overtook command with Markinson's death
- Mara Aramov: a triple agent with multiple connections; she also acted as an assassin
- Dillon Morgan: field commander for Agency operations
- Mr. Cochran: PHARCOM's second CEO
- Steven Archer: Morgan's top lieutenant and assassin
- Derrek Falkan
- Colorado Bridge Bombing Commander: A trigger man who works under the orders of Steven Archer
- Thomas Holman:
- Elsa Weissenger: a scientist who later worked for the IPCA, but joined Mara in her mission to change the world
- Ellis: US Army demolitions expert and undercover operative assigned to infiltrate Black Baton
- Jason Chance: Undercover lieutenant assigned to the CBDC
- Teresa Lipan: Former ATF operative
- Mihai Niculescu: Commander-in-chief
- Erich Rhoemer: Commander-in-chief
- Anton Girdeux: Demolitions expert who had to guard the Washington Memorial bomb
- Pavel Kravitch: Communications specialist who participated in the assault on Washington
- Vladislav Gabrek: On-site commander of Rhoemer's base in northern Kazakhstan.
- Mara Aramov
- Jorge Marcos: Secondary bomb detonator during the Washington assault