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. Yet 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 did not.
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, and finally Washington Park where he must incinerate enemy 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 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 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 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 the Ukraine to inject test subjects with a cure and locate Phagan, who is now Rhoemer's prisoner. In the catacombs, Phagan tells Gabe that Lian is alive, and they reunite. Lian now has the virus, 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 a lethal chemical, and Markinson was having them killed. Admist the fighting between the terrorists and Phagan's guards, 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 Markinson wanted the virus in the Agency's possession. He never authorized the missile attack, but before he can do anything to stop it, Rhoemer kills Markinson with a bullet to the head. Gabe must reach the missile's control center in time and destroy it. Upon doing so, he disposes of Rhoemer 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. Back in the Agency headquarters, Aramov approaches a mysterious man and whispers something in his ear. He congratulates her while the scene reveals PharCom boxes in the office.