Syphon Filter 3 is a third-person action-adventure game that follows the story of a government agent named Gabe Logan. The game is set in the near future, where Gabe must go undercover to stop a terrorist organization that plans to release a deadly virus. The player controls Gabe as he goes on a mission to infiltrate the terrorist organization and stop them from releasing the virus.

The story is divided into several levels, each one taking place in a different location in different parts of the world, including a research facility in the Arctic, a jungle in South America, and a city in Asia.

Gameplay is focused on action and stealth, with a variety of weapons and gadgets available to fight enemies and complete objectives. A cover system allows Gabe to take cover behind objects and pop out to shoot enemies, and a stealth system lets him sneak up on enemies and take them out without alerting others.

The game features a variety of gadgets that the player can use to complete objectives, such as a grappling hook and a silenced pistol to navigate the environment and take out enemies.