Nai—a young man who travels in search of another by the name of Karoku, a lone bracelet his only lead. Gareki—a willful young man who earns his daily bread by thieving and picking pockets. Thrown together at an eerie mansion, where they are entrapped and framed, Nai and Gareki are soon hunted down as criminals by national security forces. As they are driven into a corner, before them appears the most powerful defense agency in the country, "Circus"—!!

Stopping by his hometown of Karasuna, Gareki runs into his old friend Tsubame, who asks him to help uncover the truth behind a string of murders that have recently been plaguing the town. Though the crew assumes that the murders were the doing of their mutant quarry, they catch Tsubame's younger brother, Yotaka, red-handed at the scene of the latest crime. Ordering the bewildered Nai and Gareki to escape, Yogi prepares to do battle with Yotaka, but this is one fight that can only end in heartbreak for Gareki...

Nai and the crew of the 2nd Ship head for the metropolis of Vantonam, with 1st Ship's Jiki on board under Captain Tsukitachi's orders. The group takes some time off to enjoy the city, but while browsing the Nyanperona Shop, they are called out by a young boy, and...?! Later, Nai receives a secret communication with a dire message from Karoku as Circus begins planning an attack upon the "Smoky Mansion," where Karoku says he is being held. After the fierce battle ends and the dust settles, what truth will await Nai and Gareki...?!