Syphon Filter 3 continues the adventures of covert operative Gabe Logan and his team as they try to rid the world of the deadly syphon filter virus. In the wake of the events of Syphon Filter 2, Logan finds himself and his friends under suspicion from the U.S. government for committing acts of treason. As the different members of the team testify, players will reenact missions from times past, including a level that represents the events of the original opening cinema from the first Syphon Filter. As the game progresses, these missions from the past are mixed with present operations.
The story continues in this way, and players will receive new information on the government's role in the development of the virus as the plot takes its twists and turns. Players who've experienced the gameplay of the previous titles will be immediately familiar with this game's mix of third-person and first-person perspectives.