Gabriel Logan and Lian Xing were agents of the Agency (a black-ops organization), on the trail of wanted international terrorist Erich Rhoemer and his group, the Black Baton. Special agent Ellis (a less experienced Agency operative) attempted to infiltrate Rhoemer's narcotics operation in Costa Rica, but he was discovered and executed by ex-KGB agent Mara Aramov on Rhoemer's orders. Rhoemer then ordered his lieutenant Anton Girdeaux, a French terrorist, to incinerate the plantation to destroy evidence of their research. Logan and Xing arrived at the scene to find Ellis dead, the location burning, and the terrorists gone.
Around the same time, back at Washington, D.C., Edward Benton (the Deputy Director of the Agency) was giving a report on Logan's mission to Agency Director Thomas Markinson and a shadowy, unnamed figure who says of Logan, "We will wait and see what he can discover." Logan and Xing then investigated a mysterious viral outbreak in the Himalayas which may have been connected to Rhoemer somehow. They discovered that the civilians within the 100 mile range were dead, except for one man, whom Xing discovered was alive.Erich Rhoemer and his gang shortly after launched an all-out terrorist assault on Washington, D.C., unleashing murder and mayhem on the streets and in the subways of the national capital. Logan was sent in by the Agency to stop the terrorist threat. His main objectives were to destroy the Black Baton's communications uplink, disarm any bombs (including a main bomb containing an unknown virus), help CBDC (a government organization sent in to combat the terrorists and to provide demolition support), and eliminate Rhoemer and the Black Baton. He encountered Pavel Kravitch, Rhoemer's communications expert, and kills him. At the same time, he destroyed some of the Black Baton's communication equipment. After the fight, Logan gained access to the nearby subway, and — with the help of CBDC — disarmed the bombs planted by the Black Baton.
At the end of the subway was a final bomb. As Logan reached it, he realized that it had a 5 second timer, and was ready to blow. Logan escaped the blast, but it cratered blocks upon blocks of Washington D.C. As Logan advanced within the destroyed subway, he encountered Aramov (another Black Baton member) and wounds her. He found out through Aramov that the main viral bomb was being held at Washington Park.
Logan advanced to Washington Park where another Agency operative (and his team), Jenkins, was at. Logan reached the park, but Benton contacted Logan, the former explaining that Jenkins and his team were wiped out by the terrorists. Logan continued his mission through Washington Park, disarming bombs with CBDC in the process. In addition, Logan encountered the rest of the communication equipment used by the Black Baton. By using the equipment, he discovered the bomb triggerman for the Black Baton, Jorge Marcos, was nearby. As Logan advanced through the park, he kills Marcos, and enters the Freedom Memorial.
Within the Freedom Memorial was the main viral bomb that Logan had been searching for, as well as Anton Girdeaux, who was wielding a flamethrower and wore advanced armor. With Girdeaux immune to even grenades, and being warned that setting off explosives would trigger the bomb, Logan managed to kill Girdeaux by detonating the gas tanks on his back.
The Agency examined the viral bomb. They discovered that the virus was a deadly next-generation bio-weapon, capable of actually targeting specific ethnic groups while leaving others unharmed, as was so appropriately demonstrated by the Himalayas event that Logan and Xing attended earlier. The virus was so powerful that it can be programmed to target any species on the planet. The virus and the events led to the mysterious pharmaceutical mega-corporation PHARCOM and its CEO and founder, Jonathan Phagan. Logan attended the black tie gala at PHARCOM's new EXPO Center Museum. Behind the scenes, Phagan met with Aramov and Benton (whom was discovered by Logan as an Agency mole). Phagan refused to give Aramov the location of the labs containing Syphon Filter, and the former became a hostage of the latter. Benton battles Logan but is ultimately defeated. Logan made his way deeper into the EXPO Center. He managed to free Phagan, but the latter fled. Aramov was taken in by the Agency, but eventually escaped their custody.
Logan and Xing then goes on a reconnaissance and demolition mission to Rhoemer's secret base in Rozovka, Kazakhstan (the location given to them by Aramov). Logan succeeded in his mission by destroying the base, but Xing was taken captive by Rhoemer. During the mission, Logan kills Rhoemer's commander Vladislav Gabrek and destroys Rhoemer's attack helicopter. It was destroyed in an explosion that Logan believed to have killed Xing as well.
Logan headed back to the Agency headquarters, where Markinson explains that the virus they were after was called Syphon Filter. Markinson explained the effects of the virus, and decides to send Logan to Rhoemer's stronghold in Uzhhorod, Ukraine, which was a Gothic cathedral of Western European design. Logan was ordered to inject the Syphon Filter test subjects with a 'vaccine', kill Rhoemer's scientists, and to find any other information. Logan managed to find Phagan, who gives the former the location of the Syphon Filter labs. Phagan later led Logan to Xing, whom was alive all along, but was infected with said virus. Logan and Xing escaped the stronghold, but Phagan was murdered by Aramov. She willingly helped Logan and Xing, taking them to the PHARCOM warehouses in Altmaty, Kazakhstan.
Logan then infiltrated the PHARCOM warehouses where Phagan's men was battling with Rhoemer's thugs. Logan made his way to the missile silo within the warehouses where a missile that contained Syphon Filter sat. Markinson appeared and explains that his plan was to steal the virus for the Agency. Furthermore, the 'vaccine' that he gave Logan earlier actually killed the test subjects. Rhoemer then appeared and kills Markinson, stating that, "Markinson came here to stop (the missile), but he was too late." Logan advanced into the silo, and destroys the missile in midair. He then has a fight with Rhoemer, and kills the terrorist with gas grenades.
Around the same time at Washington D.C., the shadowy figure (from the beginning of the game that had been talking to Markinson) was holding a sample of Syphon Filter inside of the Agency's headquarters with Aramov. He said, "Well done my dear, well done" as Aramov laughed.
Provided is a comphrensive list of all the voice talents used in this game.
John Chacon | Gabriel Logan (voice)
Ava Fang | Lian Xing (voice)
Eric R. Hilding | Thomas Markinson (voice)
Anna Murivitskaya | Mara Aramov (voice)
Art Freedman | Jonathan Phagan (voice)
Doug Boyd | Erich Rhoemer (voice)
Frederick L. Gillette | Edward Benton (voice)
Jason Cusson | Anton Girdeux (voice)
Bob Sáenz | Additional Voices (voice)
Rahman Shamilov | Additional Voices (voice)
Joel F. Martinez | Additional Voices (voice)
Gary Barth | Additional Voices (voice)
Buzz Burrowes | Additional Voices (voice)