One day, a certain city completely disappears from the map. Three years later, a lone courier named Takuya saves Yuki, the lone survivor of Lost, and the two begin their journey to the void that was once a city.
After Takuya gets severely injured by a mysterious boy, it is decided that going straight to Lost is too dangerous. Yuki and the others try to escape, but Suzuna and the Agency interferes. And so does a dangerous knife-wielding Tama-shi.
Takuya, Yuki, and Geek get stuck in a strange pocket of space near Lost. Worried about Yumiko and Kouta, they look for a way out. But Geek comes across something he cannot believe. The members of SPR5, including Yua, appear right before his eyes.