 Taking place after Syphon Filter 2, Lian Xing is finally cured of the virus. However, Teresa Lipan got killed by Chance, making Gabriel Logan kill him. During the funeral, Gabe, Lian, and Lawrence Mujari are still trying to eliminate the Syphon Filter threat that is still going on. After killing a rebel Chinese general Shi Hao in Tokyo, Gabe and Lian escape. Lawrence manages to call the Senate and testify for themselves. The player controls the characters  past missions including the mission to Costa Rica. While one character testifies, the others are trying to save the world from the virus. Will Gabe and Lian manage to clear their names and save the world, or will they still remain fugitives? Only the player can find out.