In 1999, Gabriel Logan and his partner Lian Xing investigate a series of biological outbreaks triggered by international terrorist group Black Baton whose commander is 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 perished somehow survived. Before the Agency can pursue Rhoemer, he assaults
Washington, D.C. and threatens to detonate viral bombs scattered across the city. Gabe battles several terrorists, including Mara Aramov, as he follows the trail of bombs across city streets, subways, the
National Mall and finally Freedom Memorial where he incinerates munitions expert Anton Girdeux to stop the final threat. 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 cooperating. At the PharCom Exposition Centre, 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. 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. 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, assassinate the scientists working there, 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 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 in fact a
lethal chemical, and Markinson was having them killed. Using the fighting between Rhoemer's terrorists and Phagan's security personnel to cover his insertion, Gabe descends into a silo and searches for the missile's detonation codes. He finds Markinson, who admits that the Agency was in fact working with Black Baton all along. Rhoemer worked for Markinson, since the latter wanted the virus in the Agency's possession. He never permitted the missile attack, but before he can stop it, Rhoemer kills Markinson with a headshot. Gabe races to the missile's control centre 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. Lian asks her partner how far Markinson was in cahoots with Rhoemer and Phagan, but Gabe believes that 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. ==Development==