The Messians have begun construction of a great Cathedral to be the throne of God from which he will purge the world of sinners, and the Gaeans seek to summon Lucifer from The Abyss to release strong demons across the world. The Gaeans aligned themselves with Chaos, shunning the Messian view as dictatorial, and choosing a path of anarchy where the strong make their own futures. The Messians have aligned themselves with Law, choosing to devoutly follow the plans of their leaders to find salvation in 'God's Thousand-Year Kingdom' finding the Gaeans as anarchists. The two factions are at odds with opposing ideologies. In Tokyo, particularly, two groups have risen from the remnants of the Martial Law forces and the Japanese Rebellion forces - the Messian Order and the Ring of Gaea. Humans have survived, but the world has drastically changed, and demons roam freely. Upon their return from the Diamond Realm, they discover that 30 years have passed and that worldwide nuclear holocaust has occurred. The Protagonist, the Law Hero, and the Chaos Hero only survive thanks to the sacrifice of the Heroine, who sends them to the Diamond Realm, another plane of reality, with her magic. The Protagonist can choose to align himself with any of the three factions, but no matter what, the Heroine will be rescued and join his side, the two forces will clash, and Ambassador Thorman - the deity/demon Thor in disguise - will launch nuclear missiles on Tokyo, destroying nearly everything. Despite their efforts, she is captured by Gotou's forces and Yuriko appears to personally oversee her public execution, claiming that once she is gone, Yuriko can be with the Protagonist eternally. The party meets the Heroine, whom turns out to be the sacrificial woman from their collective dream. A third resistance faction, led by the Heroine, seeks to keep the Americans and the reactionary Japanese forces from clashing and getting Tokyo caught in the middle. A reactionary Japanese militia force, led by Gotou, rallies against the cordoning imposed by the Americans and they begin working with the demons, whom they see as the ancient spirits of the land sent to create a utopia, to prevent the Americans from destroying Tokyo. The news of demonic invasion soon gets out, however, and the American military, led by Ambassador Thorman, declares martial law in Tokyo as they try to get rid of the demons. Along the way, he meets a woman named Yuriko, who claims to be the woman he met in his dream and that she intends to fulfill her promise to always be with him as soon as she can sever his connection to 'the other one'. He soon meets up with the real-world versions of the men he met in his dream as they begin a search for some of the missing persons in the demon-infested Tokyo. Guided by the mysterious Stephen, the Protagonist uses the Demon-summoning program to convince some of the demons to join him and fight back against the more hostile demons. The woman who was to be sacrificed expresses her gratitude before the dream ends. The Protagonist has another dream in which he meets the same dream-companions again, only this time they interrupt a ritual sacrifice in the dream.
It's soon realized that recent experiments with Terminal-based teleportation have accidentally opened up a portal to The Abyss, and demons have begun roaming the streets. Outside, it becomes apparent that all is not right with Tokyo - police have barricaded many streets and people have started to go missing, along with a recent murder in the park. Intrigued, the Protagonist downloads it onto his laptop before going out on an errand for his mother. Upon waking, the story begins in Tokyo as the Protagonist checks his email to learn that a mysterious man calling himself Stephen has sent out a suspicious ' Demon Summoning Program' to all those willing to use it. The story begins with a dream sequence as the nameless Protagonist is led through a formless hallway to meet a crucified man, a man tortured by demons, and a beautiful woman bathing who pledges to be with him eternally.