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One morning in 2115, in the 17th Far East Imperial City Management District, Tohru Kazasumi wakes from a strange dream. After school that day, he is returning home with his classmate Kyoka when they see the mysterious girl from his dream by the roadside.

Tohru and Kyoka escape their crisis and return home with help from Remy Odhner. Tohru passes out in transit and wakes up in a strange institute. He is brought to Brian Odhner, who was waiting to reveal to Tohru the truth of the world…

After school, a luxury car pulls up next to Tohru. The door opens to reveal Kyohma. He offers Tohru a ride to the laboratory and then uses the time to ask Tohru his true intention for opening the case.

Tohru returns to the Management District, upset to see a comrade fall before his eyes. He’s blaming himself for the outcome, when a communication from the Timekeepers arrives and all eligible people are again summoned to fight...

After a fierce battle, both Tohrus arrive at the spot specified by Timekeepers. In the middle of a gunfight there, they’re suddenly told to stop fighting. The door at the end of the passageway opens, and they find an unexpected individual awaiting them.

The Timekeepers' power sends Tohru to an unfamiliar alley. Waking up to children's voices, he sees the Kyoka who fights for Frontier S. He’s led to the hideout of Team Bastian, where Kyoka tells Tohru about the harsh reality those in Frontier S must face.

In the culmination of recent events, a giant sandstorm has developed and Tohru is swallowed up by it. While inside, he finds his resolve to fight tested as he is again confronted by the Timekeepers.

The sandstorm continues to rampage with Remy at its center. It attacks indiscriminately, leaving both sides overwhelmed by its power. Just then, something is observed coming through the wall of sand...

After being warned of an emergency, Tohru undergoes a forced return to the present. He faints as a result and wakes up in the lab, only to find Brian Odhner waiting for him. As Tohru attempts to grasp the situation, Brian introduces him to someone...

Tohru and Kyoka are reunited with Kumi and Lyudmila’s help, and escape from the laboratory to a safehouse. Finally having a moment to rest, Tohru falls asleep and begins to dream about the mysterious young girl’s past.

Faced with the final battle, both sides head into the battlefield once more to protect the futures of their worlds. In the 2015 Shibuya that has the giant Energy Cube, the fierce all-out war begins.

Because the Frontier S Tohru cannot believe the eradication of the Timekeepers leads to true salvation for both futures, he challenges the 17th Tohru for one last battle. The ultimate showdown begins, with the two futures at stake.