The Great Destruction
The Great Destruction is the apocalypse which transpired during the events of Shin Megami Tensei and heavily influenced the world in Shin Megami Tensei II, in which most of humanity were wiped out by giant floods, supposedly a form of punishment as delivered by God.
The series of events started with the rising tensions between a Japanese resistance force and the Provisional Martial Law Government set up by the American Army after the sudden appearance of demons in Tokyo in 1999. The head of the American forces was actually a disguised demon Thor, acting under orders from Law-aligned forces. He reveals himself to the Protagonist of the first game and his party before launching nuclear ICBMs at Tokyo to suppress the demon outbreak, destroying Tokyo in a nuclear holocaust.
Thirty years later, in a rebuilt Tokyo where demons roam freely, the Messian and Gaian cults had formed. The Messian forces of Law succeed in building a great Cathedral to bring forth God’s Millennium Kingdom. This act causes a second Great Flood which again destroys Tokyo, leaving little standing apart from the Cathedral and its inhabitants.