For the video game, see Syphon Filter (video game).
For the virus, see Syphon Filter (virus)
For the franchise, see Syphon Filter (franchise).
For the theme song, see Syphon Filter (main theme)
The Syphon Filter Conspiracy was one of the most significant incidents in all of the entire series. Spanning four of the six games, it involved numerous parties and factions, all with their specific agenda. It started in the first game and did not end until the fourth. Even so, the matter carried substantial implications, not only in politics, but also in different areas, since Gabe Logan was forced to investigate into multiple places on the globe despite having ended the fiasco once and for all.
Events
Black Baton investigation
Gabriel Logan and his partner Lian Xing investigate a series of biological outbreaks triggered by international terrorist Erich Rhoemer. When fellow agent Ellis loses contact during a mission in Costa Rica, the top-secret Agency dispatches Gabe and Lian to find him. They discover Ellis is dead, and Rhoemer's suspected drug operation is a cover for the viral operation. Another outbreak in Nepal leads to more questions when an infected person who should have died remained alive.
Defense of Georgia Streets
Before the Agency can pursue Rhoemer, he attacks Washington, D.C. with viral bombs. Gabe battles several terrorists, including Mara Aramov, as he follows the trail of bombs across city streets, subways, Washington Park and finally Freedom Memorial where he must incinerate enemy munitions expert Anton Girdeux to stop the final threat.
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 working together. At the PharCom Exposition Center, Gabe shadows Phagan to a meeting with Aramov and Edward Benton, an apparent Agency mole 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. Gabe is sent on another operation, this time to Rhoemer's base, which he must sabotage.
Encroachment on Rhoemer's base
Logan successfully destroys Rhoemer's base, but Lian is captured and 'killed'. Markinson then extracts Gabe from the area.
Assault on 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. Gabe and Markinson 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. The three leave, deciding to head for the PHARCOM warehouses.
Showdown on Kazakhstan
Attempting to stop Rhoemer's missile from launching, Gabe enters Phagan's compound where he comes across intense fighting between the Black Baton infantry and PHARCOM Elite guards. 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.
Second capture of Lian
Gabe and Lian are now targets of the Agency after uncovering its connection to Syphon Filter. Agency operative Dillon Morgan captures Lian at the PharCom warehouses, forcing Gabe and the CBDC soldiers to rendezvous with ex-agent Teresa Lipan in Arizona.
Traversing the Rocky Mountains
However, Gabe and his allies are still in their plane when the Agency shoots down their transport over the Colorado Rockies, so Gabe and CBDC Lieutenant Jason Chance head down the mountain in search of their plane and a box of PharCom data disks. Michael Archer of the Agency attempts to stop them at all costs. Simultaneously, a group of conspirators, including Mara Aramov and Agency director Lyle Stevens, promise to deliver the virus to a rogue Chinese general named Shi-Hao.
Escape from the compound
Lian recovers in a U.S. air force base where Morgan and two operatives are working with Dr. Elsa Weissinger of PharCom to extract infected plasma from test subjects. Lian learns that the other subject was Phagan, who survived his gunshot wound long enough for the Agency to take the plasma. Weissinger attempts to keep Phagan alive for research, but Morgan, intending that nobody find Pharcom's CEO infected with an unknown virus, deactivates his life support.
Lian eventually escapes the medical building and interrogates Agent Thomas Holman to learn that Morgan is planning another operation to the PharCom Expo Center to find an encryption disk. She leaves the base in a helicopter and teams up with Gabe to battle Archer's forces. Gabe shoots Archer during his escape, and recovers the PharCom data.
Second visit to the Expo Centre
The protagonists follow Holman's lead to the Expo Center and kill Morgan before he can recover the disk he sought. After decrypting the PharCom data, Teresa realises that some information is missing. The other half must be with Uri Gregorov, director of the Russian SVR, who appeared at the warehouses before Gabe left. Since Lian and Uri know each other, they agree to meet in Moscow.
Shootout in Russia
Aramov instigates a gunfight while they meet and Lian pursues Gregorov. Lian later learns he is an impostor working for Mara and trying to find the other half of the data. The man confesses that the real Gregorov is in a Russian gulag, Aljir Prison, which once held Lian. Gregorov uncovered a plot to sell the virus to Shi-Hao, so Aramov intervened. Lian goes to stop Gregorov's execution, but collapses from the virus. Gabe takes her back to the States, while Gregorov promises to handle Shi-Hao.
Gabe's capture
Gabe and Teresa arrive back at the Virginia safehouse overseen by Lawrence Mujari, a freelance pathologist. They decide to trade the PharCom data to the Agency for Lian's vaccine. Director Stevens double-crosses Gabe in the Agency's New York City labs, but Logan escapes and forces Dr. Weissinger to give him the vaccine. Gabe also finds out that Chance survived the mission in Colorado, and sets him free.
"Get to the chopper!"
Pursued by NYPD SWAT cops and Agency personnel, Gabe and Teresa hurry back to their helicopter. Stevens and several Agency operatives destroy part of the streets to knock them into the sewers. Gabe and Teresa eventually corner Stevens, shooting him in cold blood. Assuming that Chance was killed since he failed to respond to radio calls, Gabe brings Teresa to the rooftop.
A traitor in their midst
They reach the helicopter to find Chance waiting in impenetrable Agency-issued super-armor. He was really working for them, and he seemingly kills Teresa. Gabe suspected it since the Agency always knew where he was in Colorado. Both men fight, and Gabe kills the man he trusted with an assault shotgun that drives Chance into the helicopter blades, decapitating him.
Hadden's agenda
A news report reveals that the Agency's existence is now public, and U.S. Secretary of State Vincent Hadden promises that the government will investigate. Gabe cures Lian and makes a grave for Teresa. He, Lian, and Lawrence hold a small memorial and promise to keep fighting, while soldiers watch them from a distance. In a post-credits scene, Hadden and Aramov emerge from a helicopter, with Aramov saying that the Administration will soon fall allowing Hadden to become President. Although he could end it here, Hadden has other plans for Gabe.
Assassination of Shi Hao
Secretary of State Vince Hadden brings in Gabe, Lian, and Mujari to testify in Congress about their relationship to the Agency. He considers all three to be guilty, and questions them after they assassinate Shi-Hao from a hotel in Japan. The three do not realize that Hadden is involved in the conspiracy, and is looking for scapegoats.
Costa Rican Incident
Gabe begins by describing the first Syphon Filter investigation. He and Lian went to Costa Rica to find missing Agent Ellis. When they arrive, the two see that Erich Rhoemer has ordered Ellis killed, but Gabe must continue his mission and identify what Rhoemer was doing at the drug plantation. Gabe chases Rhoemer onto an airplane despite his Agency superior Edward Benton warning against it. Gabe did not know back then that Benton and the Agency controlled Rhoemer, who escaped from the plane.
Outbreak in Africa
Mujari testifies next, and tells Hadden how he once worked for a resistance during the Apartheid era in South Africa. At the Pugari Gold Mine, he discovered that mining slaves had caught a deadly plague and the mine owners were covering it up. Mujari retrieved samples and gave them to Teresa.
Incursion on Afghanistan
When it's Lian's turn to testify, she mentions her first meeting with Gabe during the Soviet occupation of Afghanistan. Lian was working for the Chinese MSS, and Gabe saved her from an ambush. In turn, she agreed to distract Soviet forces so he could move a convoy of weapons into Kabul.
Scuttling the Lorelei
During Lian's testimony, Gabe goes to Ireland with Mi6 agent Maggie Powers in an effort to sink a shipment of Syphon Filter. Onboard the S.S. Lorelei, Gabe plants several explosives and finds a document that will point to a virus test site in Australia. He also looks for any information on the mysterious arms consortium that controls the Agency. With the bombs set, he and Maggie leave the freighter.
While Lian is describing how she met Elsa Weissinger at the Costa Rica mission, Gabe and Maggie fight IRA terrorists looking to take the virus themselves. Gabe uncovers a mole in Mi6, Nigel Cummings, who is aiding them. He kills Nigel and secures the last viral transport on the docks. Then they sink the S.S. Lorelei.
Rendezvous with Benton
Back in Washington, D.C., Gabe talks about his first meeting with Benton in Afghanistan. Benton claimed to be a CIA agent transporting weapons to Afghans rebelling against the Soviets, but when Gabe and Ellis escort the convoy, the Afghans attack them. Gabe gets into Kabul and meets Lian, who sets up the diversion. However, a tank gets in their way, so Gabe destroys it. He learns that Benton was supplying arms to the Soviets, and was really an Agency operative.
Second operation with MI6
As Hadden questions Gabe, Lian teams up with Maggie to kidnap Elsa from the Australian test site. Elsa is ready to betray the conspirators since Aramov left her behind, and she has Lian assemble a vaccine for aborigines held captive by Commander Silvers. Silvers plans to kill the test subjects, so Lian kills him first. When she returns to Elsa, Lian finds her gone.
A spider's web of corruption
Hadden accuses Gabe of lying. He thinks Gabe murdered Teresa Lipan, but Teresa surprises him by appearing in person. Chance had only injured her, not killed. She describes her first meeting with Gabe during her time as an officer with the Bureau of Alcohol, Tobacco, and Firearms. A group of NSA agents headed by Colonel Silvers were posing as FBI to eradicate a private militia that had recovered data from a government satellite. Gabe, as an Agency operative, saved her life, and helped her when she rescued the wife and son of the militia leader. She left the ATF and joined the Agency.
Second capture of Mara Aramov
Teresa faked her death to find the people behind the Agency. Her investigations into Aramov yielded a connection to Vince Hadden himself. Before Gabe can arrest him, Mara kills Hadden. She and several consortium terrorists take over the Senate building, but Gabe prevents her from detonating any explosives. He chases her onto a train full of hostages, and wounds her, thinking it will do.
The Agency is reformed
In a post-credits cutscene, Mara escapes later on. Gabe promises he will find her, but for now the Syphon Filter crisis appears to be over since the death of Hadden. Gabe will become the new Agency director, and free it from corruption. Little does he know that an operation is ongoing near the S.S. Lorelei's wreck site. People are recovering the viral crates.
Syphon Filter version 2
The past returns when Syphon Filter reemerges as the deadlier Omega Strain. A Chechen officer named Mikhas Ivankov is selling it on the black market, and outbreaks are occurring around the world. The man behind the conspiracy, Mihai Niculescu, sends Mara Aramov to find and eliminate him. Meanwhile, Gabe and the Agency split up and investigate locations of certain outbreaks.
Chaos in Carthage
An Agency team headed by Imani Gray visits Carthage, Michigan in search of Mujari, who disappeared while investigating Dr. Richard Broussard. Broussard had made a deal to give the virus to terrorists from the Anarchiste Liberation Army, but he backed down. The ALA acquired it anyway, and attacked the city. Imani and her team rescue Mujari to find the Omega Strain has infected him. The agents defeat the ALA leaders: Andre Proust, Soren Masson and Jean Fournier, then prepare for their next assignment. Investigating an Ebola outbreak in Uganda with Lian, Gabe shows his obsession for stopping the Syphon Filter conspiracy.
Assassination of Dimitri
IPCA commander Gary Stoneman tells the Agency operatives about his history as an assassin for the CIA, and how he recently killed mafia leader Dimitri Alexopoulous to keep him from obtaining the Omega Strain in Italy.
Belarusian Mayhem
The team follows Stone to Belarus and tracks a shipment of infected cattle which leads to the residence of Ivankov. They discover that his courier Yuschenko is selling the Omega Strain, and Agency pilot Alima Haddad ends up captured by the Chechens. Stone assumes the worst, presuming she was killed.
Transaction on Kyrgysztan
Lian later tells the Agency team how she identified that North Koreans were attempting to purchase the virus. She infiltrated the domain of warlord Askar Saydahmat and found his people were about to give the Omega Strain to Sok-ju Yang, with a Yemeni terrorist being present as well. Lian eliminated all the involved parties.
Yemeni Trouble
Gabe enlists help from Ehud Ben Zohar of the Israeli Mossad upon determining that Yuschenko plans to sell the virus to Fatha Al-Hassan, a Yemeni leader. Zohar only cares about stopping the man's terrorist connections, so he steals the viral canister after the Agency retrieves it from Yuschenko, and uses it to force Gabe's people into helping his mission.
Zohar and the team enter Al-Hassan's palace disguised as the dead Chechens. After Zohar eliminates Al-Hassan, he searches for evidence of weapons contracts while the Agency personnel defends him. He does not find anything, but Stone arrives to rescue them, and reveals that Gabe sent him in case Zohar tried any tricks. They exchange the contracts for the virus.
Surveying Jandran
Next, the team investigates a lead recovered from the Belarus operation that shows Dr. Nikolai Jandran is conducting virus tests. Maggie Powers assists them in breaking into Jandran's labs and recording evidence. The team escapes before enemy forces destroy the university where Jandran works.
Genocide on Chechnya
Mujari, having recovered from the virus, explains his own investigation into the Chechens and why Ivankov wants independence from Russia. He sees that Uri Gregorov and other Russians are imprisoning the rebels, and finds hints of atrocities. Mujari knows both sides have reasons for what they do, thus the situation is not black and white.
Final destruction of the Lorelei
Afterwards, Mujari takes control of the Agency team as they check the wreckage of the S.S. Lorelei. The university turned up salvaged boxes, indicating an undersea operation. Mujari requires that his team incapacitate innocent guards, and he evacuates the salvage rig before the Agency's planted nukes destroy the viral containers for good. However, Jandran dies from a serum before he can be brought back for questioning.
A Japanese connection
While Gabe faces pressure from the president and Alex Birchim of the White House Internal Affairs, he sends Lian and the team to track North Korean agent Yong-jun Kim, a man connected to Murakawa Industries in Japan. The investigation reveals that Murakawa, a part of the Yakuza, was helping to develop the Omega Strain. Aramov arrived before Lian and forced Murakawa to commit suicide for trusting Kim. Kim pretended to work with Murakawa so he could get the virus.
Recovering Imani Grey
Unfortunately, the team hears tragic news after destroying the Japanese labs. Imani had been tracking Kim on an airplane that crashed in Myanmar. Out of guilt, Lian takes the team to recover her body and the viral sample Kim was carrying. Despite claims that inclement weather brought down the jet, they find evidence indicating that Aramov had paid the Myanmar army to shoot down the plane.
Defying the White House
Gabe becomes frustrated with his investigation into the secret corporation Meta Global Funds, which he believes controls the Syphon Filter conspiracy. The purchase of Murakawa Industries by Meta Global was possible through Niculescu Funds, headed by international banker Mihai Niculescu. He is powerful and influential, but secretive as well, so Gabe suspects he is behind Syphon Filter. Against Birchim's commands, Gabe brings the Agency team to the Niculescu Funds headquarters in Zurich. They break in and find evidence linking Birchim to bribes, but nothing implicating Niculescu.
Rescuing Mara Aramov
Gabe will later describe the rest of his investigation to the Agency team, and how he looked into Niculescu's Montenegro estate in a final effort to expose him. Although he did not find physical evidence, he learned that Mara was working for him, but Mihai betrayed her. Mara did not want Ivankov to destroy Moscow, for he traded the Omega Strain to the North Koreans for a nuclear weapon.
The final showdown
Having learned of Ivankov's location from Mara, the Agency mobilises to his base and works to prevent the missile's launch. Stone recovers Alima, injured but alive, and the team works with Gabe to disable the nuclear weapon. Ivankov is eventually killed during a fight with Gabe when the enemy attempts to escape through the forest.
Depending on the player's actions, the base is destroyed and the missile launch is prevented, or the nuke detonates in the ocean. Dr. E and Mujari cure the Omega Strain and destroy the final traces of Syphon Filter. Criminals eliminate Niculescu after an Agency computer virus erases the money of his illegal clients. Government officials arrest Birchim after Gabe shows the President files linking Birchim to bribes. The conspiracy is over, and Gabe can focus on other threats. Just when it seems all is well, Dr. E resigns from the Agency, confessing that she had met Mihai Niculescu before. She intended to kill Jandran as well, believing that her destiny is to change the world. Elsa exits from the Agency base, and Gabe wonders what will happen next. A view of Stone's scope zooming in on Aramov speculates that the former is sent to assassinate the latter in the next game.
Aftermath
With the exceedingly cunning Mara Aramov finally terminated by Stone, Gabe is at peace until another terrorist organisation dubbed 'Red Section' assaults KemSynth Petroleum. Forced to investigate, Logan brings his team into the area. He would eventually be sent out to multiple locations in an attempt to stop the enemies, and would go back into action some time later when it seemed Lian Xing was a double agent.