The game is played in a first person perspective, instead of the third person viewpoint of the four preceding titles, and is also the first game in the Conflict series which does not feature four main characters. Denied Ops is based around two CIA operators, each having his own weapon and style: a former Marine and sniper named Lincoln Graves who uses an SR-25 with an undermounted M26 MASS, and a machine gun operator named Reggie Lang who uses an M249 PARA with an undermounted M203 grenade launcher.

In single player mode, the player can switch between controlling each agent. In co-op, each player controls one agent. The agents only use their weapon of choice, and cannot pick up enemy weapons. Ammunition for firearms is unlimited, but explosives are not and must be replenished at resupply boxes found throughout the levels.