Shadow Ops: Red Mercury is an action-oriented first person shooter based on modern military weapons, equipment and tactics, although presented as a "blockbuster action movie" rather than a hardcore realistic military simulation. Players proceed through linear levels while battling terrorists and hostile enemy soldiers in locations spanning all around the globe, such as Syria and France, using an assortment of modern firearms.

The player takes the role of Captain Frank Hayden, an elite Delta Force operative and the former leader of Black Saber, the President's personal black bag unit. Hayden and his team are attempting to recover a briefcase nuclear bomb code named "Red Mercury" from terrorist mercenary Vladimir Styanovich, known by his Nom de guerre "Vlady the Vicious", who is operating out of a coastal Syrian town. The team's Black Hawk is shot down immediately upon insertion, and they fight their way through the streets in pursuit of Vlady. Hayden is too late to stop Vlady from escaping via helicopter, but manages to damage the helicopter's rotors with small arms fire. Vlady, escaping over the ocean, states he is nobody's martyr, and attempts to disarm the nuke and "re-evaluate". To his dismay, the bomb rearms itself seconds later. Vlady leaves the bomb on the helicopter and leaps into the ocean in a futile attempt to escape the blast. The blast wave from the nuke kills Vlady and capsizes the U.S. aircraft carrier which had been Hayden's base of operations, as well as destroying the helicopter sent to extract Hayden's team, knocking them unconscious.