The protagonist and Naomi travel deeper into the sewers and find a place called 'The Mesh', an underground area full of self-sufficient citizens who have given up their identities above ground to live a more peaceful life.
They are soon confronted by a black-ops squad (secretly sent to destroy the creature from the lab), but the creature wipes the team out within seconds. They both flee the train wreck when the creature starts systematically killing everyone left alive on board. The only survivors of the crash are the protagonist and a schoolgirl named Naomi Sugiura. Time passes and the protagonist's train is derailed by the creature roaming the tracks, as if purposely being drawn to that point. He soon mutates into a zombie-like creature and makes a bloody exit towards the subway system. There, a symbiotic lifeform breaks free of its confines and attacks a research scientist. As he contemplates why they want to kidnap him specifically, the scene changes to a secluded research station. The game opens with the protagonist fleeing from a group of notorious cult members through the city streets and escaping on a late-night subway train. Tokyo at the end of the millennium is a megapolis with a huge system of subway tunnels and sewers.
