Sion's life turns upside down on his 12th birthday when he aids a fugitive named Nezumi. Four years later, their paths cross again as Sion unravels the dark secrets hidden within the utopian city of No. 6.

Many years ago, after the end of a bloody world war, mankind took shelter in six city-states that were peaceful and perfect... at least on the surface. However, Shion-an elite resident of the city-state No. 6-gained a new perspective on the world he lives in, thanks to a chance encounter with a mysterious boy, Nezumi. Nezumi turned out to be just one of many who lived in the desolate wasteland beyond the walls of the supposed utopia. But despite knowing that the other boy was a fugitive, Shion decided to take him in for the night and protect him, which resulted in drastic consequences: because of his actions, Shion and his mother lost their status as elites and were relocated elsewhere, and the darker side of the city began to make itself known. Now, a long time after their life-altering first meeting, Shion and Nezumi are finally brought together once again-the former elite and the boy on the run are about to embark on an adventure that will, in time, reveal the shattering secrets of No. 6.—MAL Rewrite

Sion is a bright teenager living a comfortable and promising life inside No. 6, one of this six remaining city-states created by The Babylon Treaty after the last great war devastated the world. On the rainy evening of his twelfth birthday, he meets a savvy adolescent who calls himself "Nezumi" (Rat) and is desperately trying to runaway from the authorities. For helping a fugitive of the state, Sion is stripped of all his privileges. Four years later, they meet once again. For better or for worse, Sion is about to unravel the secrets guarded deep inside No. 6.—Anime News Network