The stakes are higher in this sequel to Soldier of Fortune. The player is John Mullins, a patriot, weapons specialist and anti-terrorist mercenary, who takes on a new threat bio-terrorist organization and their Gemini virus. His mission is to neutralize the terrorists before they unleash the virus.

Soldier of Fortune II: Double Helix features over 55 levels and an all new Random Mission Generator mode. The game uses the Quake III: Team Arena engine with GHOUL II technology and its models are designed with 36 damage zones along with 16 dismemberment zones.