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.

Takuya is sent to ICU and Yuki is traumatized from hurting her little brother. Unbeknownst to them, various people have started taking action. Some have appeared to help. To find the truth. While others work to keep the plans of the Agency moving forward.

Yuki fights with Souma in hopes of bringing him back to his senses. However, sometimes it is hard to understand the true feelings of your siblings. Just when they think they've cornered Souma, he summons and attacks with Tsubasa.

With help of their allies, Yuki and Takuya manage to enter Lost. As soon as they enter, they fall in a whirlpool of their own memories. The voices of their friends and their bond to each other are the only things that can keep them moving forward.

Takuya and Yuki manage to keep themselves together as they enter Lost. They find Taiyo trying to eliminate Yuki's father, Daichi. As Daichi fights back, he reveals to Yuki that he had prepared everything for her and that she must now make a choice.