Plot

The sequel to Syphon Filter (1999) takes place right after the first one. The Agency has apparently betrayed Gabe Logan and framed him for the Khazakstani ICBM missile launch containing the Syphon Filter virus that was destroyed by him.

The sequel to Syphon Filter (1999) takes place right after the first one. The Agency has apparently betrayed Gabe Logan and framed him for the Khazakstani ICBM missile launch containing the Syphon Filter virus that was destroyed by him. Upon that, they have captured his partner Lian Xing; who was infected with the virus. As Gabe and some fellow GI's seek refuge from the Agency, their plane is shot down in the Colorado Rockies where Gabe and Lian exchange story paths while in contact with their friend and ex-Agency operative Teresa Lipan.—jondaman816

Gabe, Lian, and a squad of CBDC agents attempt to leave Kazakhstan after gathering Jonathan Phagan's back-up files only to be ambushed by the Agency; consequently, Lian is captured. The SVR arrives to cover Gabe's tracks, as he attempts to swap the data for Lian's vaccine from the Agency.

Gabe, along with the CBDC agents, are shot down by fighter aircraft over the Rocky Mountains while en route to Arizona to rendezvous with former Agency operative Teresa Lipan. Gabe and the CBDC agents parachute to the ground. Phagan's data disks remain on the plane, however, and it crashes somewhere in the Rockies. With the aid of Lieutenant Jason Chance, John Ramirez, and other CBDC agents, Gabe locates the crash site containing the information on the Syphon Filter virus on the disks, while fighting off pursuing commandos. Meanwhile, Lian sabotages the Agency's pursuit of Logan, interrogates Thomas Holman, kills Falkan, and flees from McKenzie Air Force Base in Colorado. Having requisitioned a UH-60 Black Hawk helicopter, Lian regroups with Gabe, transporting him to the crash site. Gabe parachutes over the crash site, attempting to surprise the ground forces. He kills Steven Archer and recovers the disks, learning afterwards that Teresa lost contact with the CBDC agents while flying to Arizona.

Despite having the disks, they are useless without the encryption codes. Lian's intelligence from Holman leads them to the Pharcom Exposition Center in New York City. Gabe infiltrates the Expo Center and finds the Agency covering their tracks. After fighting his way through the Expo Center, Logan manages to lock himself up along with Dillon Morgan, who has obtained the codes. Morgan has rigged the center with explosives. Teresa diffuses the explosives, while Logan kills Morgan and retrieves the codes. When the encryption disks are analyzed, it turns out that they only have half of the encryption data, and that the other half was in Uri Gregorov's possession. A meeting is set up in a nightclub in Moscow, with Lian unaware that she was meeting an impostor hired by Mara Aramov. Aramov's thugs instigate a shootout; Lian chases and incapacitates the impostor. However, SVR officials capture him and the protagonists bringing them to SVR headquarters.

The main characters learn that the real Gregorov is being held in Aljir Prison, located in a remote region of Siberia, and the background of their Agency, which originally served as an international arms consortium that has sold weapons to a multitude of terrorist groups, with implications surpassing that of the Iran-Contra scandal. The Agency was trying to sell the Syphon Filter virus to a rogue Chinese general named Shi Hao, attempting to lead a rebellion in the Heilongjiang province, a conflict which will provoke the Russian military into action, as this region has been contested by Russia and the People's Republic of China. Lian infiltrates the prison to rescue Gregorov, knowing the layout from her previous imprisonment. She sabotages the electrical system to stop the execution, inadvertently starting a riot. Lian makes her way to the execution chamber and frees Gregorov. They fight their way out of the prison, only for Lian to collapse during extraction. Finally in possession of the complete data, Gabe attempts to negotiate with Lyle Stevens.

Gabe arranges a meeting at the Agency's New York laboratory to retrieve the vaccine. He believes that Stevens will double-cross him and eventually the latter does. Elsa Weissenger injects him with a drug to knock him out. After killing the scientist that was about to extract his plasma, Logan is free to move about the facility. He learns that Chance and Ramirez survived in Colorado and were taken by the agency. Gabe frees Chance from his cell and tells him to save Ramirez and run. Gabe eventually locates Weissenger and recovers the vaccine. The security alarm then goes off and allows Weissenger to escape. Logan escapes the lab in a protracted pursuit by Agency operatives.

Back on the street, Gabe finds out that SWAT has been deployed in the area because of the shootout in the agency labs. He makes his way to an apartment terrace (while helping a pinned down SWAT team clear 3 snipers from a slum building along the way) where he assists a female SWAT officer in killing 3 more snipers which have pinned down her wounded partner. Shortly after aiding her, Gabe learns that Chance failed to show up at the extraction point, and assumes that he is dead. Stevens then shows up, holding the female officer hostage. He executes the officer and attempts to kill a surrendering Gabe, but Teresa detonates C4 under the floor beneath them to facilitate Gabe's escape.

Logan and Teresa fight in the sewer system past Agency operatives, making it to a connected parking garage where they confront Stevens and his men. Stevens is finally cornered at the top floor of the garage and executed. As the pair go to the helicopter, they find Chance, dressed in heavy armor, having been working undercover for the Agency the entire time. He aims a gun at Gabe, but Teresa blocks the bullet, and is seemingly killed. Chance and Logan enter into a shootout, with the latter using a USAS-12 to blast his enemy backwards into the helicopter's rotors.

Gabe cures Lian with the vaccine, and mourns the apparent loss of Teresa with Lian and Mujari.

After the credits, Secretary of State Vince Hadden and Mara carry out a raid to capture both Gabe and Lian. Instead of following through with the raid, Vince chooses to have them testify before Congress, to blame them for the shootout in New York as well as all of the agency's wrong doings.