The general "story" of the missions in this set is that Shinra has uncovered a new set of caverns near the northern cave. Investigation is wrought with difficulty due to both Genesis and Wutai remnants attempting to loot the caverns, as well as the presence of the local monster population, which is strangely overpowered. Machines, infantrymen, and others are used to protect the civilian employees, but a mysterious force seems to turn both defeated machines and humans against their former side.