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, 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, Lian, Logan, and Teresa, bringing them to SVR headquarters.
The protagonists 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 survived in Colorado and frees him from his cell. Gabe eventually locates Weissenger and recovers the vaccine, only for the latter to alert the security personnel. Logan escapes the lab in a protracted pursuit by both Agency operatives and the NYPD SWAT team. He makes his way to an apartment terrace where he assists a female SWAT officer in killing snipers which have pinned down her partner. Shortly after aiding her, Gabe learns that Chance failed to show up at the extraction point, and assumes that he is dead. Stevens holds the female officer hostage. He executes the officer and attempts to kill a surrendering Gabe, but Teresa detonates C4 to facilitate Gabe's escape.
Logan and Teresa fight past Agency operatives, making it to a 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 undercover for the Agency. He aims a gun at Gabe, but Teresa blocks the bullet, and is apparently killed. Chance and Logan enter into a shootout, with Gabe using a USAS-12 to blast Chance backwards into the helicopter's tail rotor.
Gabe cures Lian with the vaccine, and mourns the loss of Teresa with Lian and Mujari.
After the credits, Secretary of State Vince Hadden and Mara carry out a raid to capture both Logan and Lian. Instead of ending it all once they were captured, Vince chooses to have them testify before Congress, leading to the events of Syphon Filter 3
One of the newest features introduced in Syphon Filter 2 was the Multiplayer game. It was considered to be an enjoyable add on by fans. More info on Multiplayer can be found here.
Syphon Filter 2 recieved mostly positive reviews from game critics and game sites.
- IGN rated Syphon Filter 2 with an 8.9 of "Great" and praised it for it's slightly tweaked gameplay, improved graphics, more missions and multiplayer mode. However it was criticized for it's familar gameplay to it's predecessor, it's trial and error trend, and confusing storyline, the IGN reviewer remarked "it's like a C+ movie script." The IGN reviewer then closed with: "So, would I would buy the game? Absolutely. It satisfies that primal videogame urge to sneak around and snipe enemies, or to simply blow them away. It's still a great action game."
- Gamespot rated Syphon Filter with 6.6 of "fair" Gamespot, being less genrous, also criticized it for it's similar gameplay to it's predecesor, storyline and it's multiplayer, stating: "the control, camera angles, and overall feel of Syphon Filter don't lend themselves very well to a mulitplayer component." the reviewer closed with: "If you were a big fan of Syphon Filter, you may get a kick out of the sequel, but the lackluster mission design and super-convoluted story really cancel out the improvements to the game's control. If you missed the first game, it's a much better (and likely cheaper) game than Syphon Filter 2." Other users and critics obviously disagreed with these results by rating Syphon Filter 2 with scores such as 8.8 and 8.9, however since they are not the official reviewers of the game, their reviews will go uncredited.
- John Chacon: Gabriel Logan
- Zoe Galvez: Lian Xing
- Shannon Tilton: Teresa Lipan
- Peter Kepler: Jason Chance
- Andrea Satin: Elsa Weissinger
- Jay Styne: Steven Archer
- Bryan Session: Lawrence Mujari
- Elina Filipova: Mara Aramov
- Bill Glanting: Dillon Morgan
- J.S. Gilbert: Uri Gregorov and Imposter Gregorov
- Dan Kennedy: Lyle Stevens
- David Caffey: Gershon
- George Joyce: Thomas Holman
- Mark Atherlay: Derrek Falkan
- Dennis Cheng: Shi-Hao
- Jason Cusson: Anton Girdeux
Following cast played additonal voices:
- Mike Benton
- Leo Chleyapov
- Chris Colon
- Shawn Dobbins
- Ryan Eames
- Otto Halboth
- Trenton Haskins
- John Koller
- Biraj Lala
- Grant Luke
- Andrei "Andy" Marcon
- John Miewald
- Conner Morlang
- Derek Quakenbush
- Shirley Tang
- Jay Vo
- Diana Zlatina
- Roy Allen
- Robert Hernandez
- Chris Johnson
- James Miller
- Jim Wallace
- According to what Vince Hadden says in the intro. Syphon Filter 2 takes place only four hours after the Original Syphon Filter.
- In the intro, Logan kills a total of eighteen Spook Commandos.