Spy Drops puts the player in the role of a counter-terrorist operative tasked with neutralizing an eco-terrorist organization intent on erasing all of the world's digital records. The group's actions threaten to return society to the pre-digital era. As the missions progress, the operative begins to question his or her goals, uncovering a conspiracy that goes beyond the initial threat. The story revolves around themes of cyberterrorism and society's adaptation to new technologies, set in military bases, jungles, and deserts.