Silent Scope 3 contains an original story mode with numerous new areas created exclusively for the PlayStation2. As an added bonus, all 14 missions from the smash-hit arcade game Silent Scope EX are also included. In a Silent Scope series first, an innovative 3-D sound system can be used to help spot and target enemies. Rounding out the features, hidden options can be unlocked and multiple endings and paths add replay value.

The game opens with Falcon raiding a drug smuggling ring at a harbor. He also battles with Cobra once again. The reason for Falcon working with Marine Colonel Robert is that the terrorists have kidnapped cloning researcher Dr. Scott, and hope to use that cloning to set off a genocide plot. Falcon's objective is to capture the terrorist cells. He first heads to a research lab to rescue hostages that are meant to work with Dr. Scott and fights a flying assassin named Mosquito. The terrorists try to retake the weapons that were seized at the port out to sea, but Falcon intervenes and shoots down an armed plane piloted by Smith. He next infiltrates a casino fronted by the terrorists for cash operations. Falcon also has to fight the casino's owner, Shaker. The terrorists then try to blow a dam bringing along a mercenary named Bull. Col. Robert also hears of profits being made for oil, as terrorists are drilling for it. Falcon shuts down the operation and fights another sniper named Ray. The weapons that would have been exported were produced at an ironworks factory that was overtaken by the terrorist gang. The sniper infiltrates and captures the factory then fights a rocket launcher assassin named Charly.