Syphon Filter: The Omega Strain is the fourth installment of the Syphon Filter franchise, and the first one to be released on the PlayStation 2 system. Instead of playing as Gabe Logan, the exiled agent from the top secret Agency, players will create their own character, which is a new recruit for the Agency.
Following the destruction of the first Syphon Filter virus, the Agency has received a new cover as the International Presidential Consulting Agency, dedicated to battling terrorist enemies. Gabe Logan, as Commander-in-Chief, has hand-picked a team of leaders and agents for his new organization, including Lian, Teresa, Mujari, Dr. E, and more.
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.
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.
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. 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.
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 seemingly innocent Yemeni terrorist being present as well. Lian eliminated all the involved parties.
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. Stone arrives to rescue them, and reveals that Gabe sent him in case Zohar tried any tricks. They exchange the contracts for the virus.
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.
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.
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.
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.
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.
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.
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.
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. However, cutscenes that play show these definite scenarios:
- 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.
- Dr. E resigns from the Agency, confessing that she had met Mihai Niculescu before and had a romantic relationship with him.
- 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.
- IPCA European Command: Training Centre
- Carthage, Michigan: Quarantine Zone
- Carthage, Michigan: Warehouse District
- Carthage, Michigan: Carthage Mall
- Pescara, Italy: St Cetteo's Square
- Mazyr, Belarus: Krivorozhstal Mill
- Mazyr, Belarus: Belaya Vezha
- Tash, Kumyr, Kyrgysztan: Saydahmat's Village
- Sana's, Yemen: Arms Bazaar
- Sana's, Yemen: Taherir Palace
- Minsk, Belarus: International University
- Samaschki, Chechnya: Ivankov's Home
- North Atlantic: Lorelei Salvage Rig
- Tokyo, Japan: Murukawa Tower
- Taguang, Myanmar, Irawaddy Basin
- Zurich, Switzerland: Niculescu Funds Tower
- Budva, Montenegro: Niculescu's Villa Estate
- Kiev, Ukraine: Chechen Terrorist Base
- This is the first Syphon Filter game where Gabe is seen on the cover page, but playable only on the last bonus mission.
- Montenegro is the only bonus level where the player can lose stealth but still continue with the mission.
- Somehow, the SMAW does not damage the tank in Belarus 2, and only anti-armour frag grenades will destroy it. Stone's version however is capable of inflicting harm on it.
- The SMAW can be seen being used by a Japanese goon in Tokyo, but the player can find no such weapon on the rooftop.
- It is strange that only Imani Grey's and Yong jun Kim's bodies are found inside the Myanmar rainforest, given the fact that hundreds were killed in the plane crash.
- The founder of Sony Bend is Mark Blank - He is the genius behind the classic text adventure, "Zork."
- The Carthage stages were rather out of place because they were originally supposed to be set in Toronto. Canada officials weren't happy with that idea, so it was switched to Michigan - but the city doesn't exist. There is a Carthage in the nearby state of Illinois, but not in Michigan.
- A triple head-shot is possible - and by extension, anything beyond that can theoretically be done.
- If a stage is completed offline, players can access the next mission online, and vice versa. The only exceptions to this are the bonus levels which are unlocked by obtaining par times for a certain episode, and the Lorelei salvage rig, which is unlocked by completing Minsk.
- The highest rank attainable playing only offline is C6, and only online, C1.(The rank C2 can be attained by using a bug that allows the player to make jumps only possible on the online mode and reaching high places for objectives, the bug doesn´t work on Mazyr, Belarus: Krivorozhstal Mill, Mazyr, Belarus: Belaya Vezha where it's not possible to obtain the par time) .
- In multiplayer games, the host can kick others out using the options menu from the pause screen.
- This is so far the only Syphon Filter game in which dying will continue the mission. The only exceptions are the bonus levels.
- This is by far the first and only Syphon Filter game which introduced the concept of par times, in which missions must be completed within a time limit.
- It also introduced a number of conventions that carried over to Dark Mirror and Logan's Shadow:
- Dead enemies will 'turn' into boxes rather than actual corpses.
- Players are limited to five weapons at the most at any one time unlike the trilogy.
- There is an equipment selection menu before every mission.
- Ratings significantly increased the replay value.
- Stone was clearly seen aiming at Mara, who is alone on her safehouse balcony, during the post-credits cutscene. Yet in Dark Mirror, he sees her inside the house, and she is arguing with Elsa Weissenger, who was absent from The Omega Strain's version of this event.
- Furthermore, why on earth would Mara have bodyguards (in Dark Mirror) when they were also absent (in The Omega Strain)?
- The M16A1 does not have any visible suppressor, but the sound it generates is that of a silenced weapon. In fact, it should not have such little noise.
- Fadhil's fate is left unresolved; the player encounters him in the arms bazaar in Yemen, and may choose to kill him, but he is never seen outside of this mission.
- Why would Mujari use an Advanced Combat Rifle during the mission on the Lorelei salvage rig if he claims to only kill in self-defense? (A similar issue is raised in Syphon Filter 3's Africa missions, where he conducts a killing spree despite having a deep personal aversion to violence).
- This question is answered in the mission briefing. Mujari states that "I am a pacifist, but I am also a realist." Mujari goes on to express his desire not to kill, but his willingness to, if need be.
- On a similar note, why would Gabe use lethal force against Niculescu's mercenaries in Montenegro if he claimed he would not kill them until he knew the art collector was behind the entire Syphon Filter conspiracy?
- It should be noted that the player can choose to knock out nearly all of the mercenaries although Gabe is forced to kill Mara's two guards to prevent them from killing her.