After the world population and economy is devastated by simultaneous hyper-hurricanes, many different factions and fledgling nations appear. In Japan, an elite class called Logos appears, controlling special zones in the country which have most of the wealth and resources. The Logos exercise control over the Levinas, the lower class which struggles day to day in order to stay alive. The Levinas are restricted from entering the special zones, causing tension which creates a resistance group which fights back against the Logos.
With the tagline "A Near Future Late-Shogunate Action Animation", the story draws analogies with 19th Century Japan at the end of the Tokugawa Shogunate period, just before the Boshin War.
Jō and Jin escape from Phantom, an elite military group which is used to control the Levinas. When they escape, they take a young girl named Sana with them. The series follows them as they work to avoid being caught by Phantom and the regular military forces of the Logos. 12 episodes.