Sixty-seven years after the events of the Subterranean Era in prior games, Earth's second largest corporation, Zio Matrix, acquires plans for a research project on Mars, dating back before the Great Destruction. Using these plans, Zio sends a research team to Mars to begin the Terraforming Project, which causes the Martian surface and atmosphere to approximate that of Earth. Other corporations learn of the project and quickly follow Zio Matrix, bringing with them the competitive environment that existed on Earth, and the employ of the mercenaries of Nerves Concord. As the three companies' war comes to a close, the most powerful, Zio Matrix, attempts a coup against the government, which has regained control through its elite mercenary team, The Frighteners, led by Leos Klein. But in the chaos that ensues, the Frighteners turn on the government, assassinate the new leader of the LCC, and take control of powerful Disorder technology. The player character is tasked with confronting them and saving the human populace of Mars.