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.

With the recent discovery of Tsuki's Tears, the famous magician Yoshiaki appears before Takuya. He asks for help in capturing Tsubasa, leader of the phantom thief brigade X. With doubts in their heart, Yoshiaki and Yuki both chase after their family.

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.

Takuya comes into contact with his past, a failed mission at the Light of Hope Academy for Disabled Children. As they step inside, Takuya and the others fall into another pocket of space. They have one goal, find evidence to bring down Lacuna.

Takuya and the others have decided to infiltrate Lacuna Chemical Laboratory, in order to drag the Agency out into the open. With the help of Yoshiaki, they use public media to draw attention to the company's wrongdoings and spur the police to move.

Amongst the volunteers, only Daichi, Taiyo, and Tsuki survive. The three of them begin working on Project Noah, in order to save millions of their people. As Daichi continues his research, he meets a woman named Miyuki and begins to question his actions.

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.