A meteorite with an alien infestation heads towards Earth following the events in Contra: Legacy of War. The meteorite falls near a Mayan temple somewhere in South America, and shortly afterward, the temple is occupied by an alien life form staging an invasion, as the natives begin to disappear and the local wildlife is devastated. After the initial side-scrolling stage, the game switches to a behind-the-shoulder view, as the commando hero Ray shoots and jumps through fully 3D environments.