In the middle of 21st century, the global warming changed Tokyo into a tropical city and the devastating squalls made it impossible to live a civilized life in the city. The government decided to abandon Tokyo and evacuate people to a gigantic layered megalopolis "Atlas," but the small capacity of Atlas gave rise to a huge number of refugees and the anti-government guerrillas. Houjyou Kuniko, the leader of the guerrilla, took up the arms and confronted the government to stop the Atlas project.

Shangri-La is based on Eiichi Ikegami's novel of the same title.