Jail, Lynn and Pele enter the town of Linden and discover that its inhabitants were annihilated by an unknown entity. Jail is confident that Licht must know something about this.
Licht and Mizuka have returned to their normal selves. While the ladies in the group suffer the consequences of Licht and Mizuka’s unresolved Star Stake, Jail receives an order to report to the supreme commander of the military.
Nana sends Jail, Lynn, Pele and Hina 300 years back in time. They arrive at an unknown institution with technology far superior to the world they are accustomed to, and meet Rihito, a young man Hina is convinced is Licht himself.
The time travelers settle into their new role as students in the military academy. However, when Schmerman reveals the "rules" of the school, it becomes apparent that there’s more to this place than fun times and friendship.
A voyeur is regularly sneaking a look at the girls’ bath, and the students are tasked with catching the culprit. Meanwhile, Jail attempts to find out more about this timeline and figure out why Nana sent them here.
Jail discovers more secrets about this world through Nana, but is intercepted by Alan during his escape. Meanwhile, the students of Class A come closer to realizing their dream of becoming a military force that does not take human lives.
Rihito decides to receive the operation to turn him into an Ace. This is the decisive moment in history that the time travelers wanted to change, but knowing what they know now, they cannot agree on what is best for everyone.
Jail and the squad are successful. With his newfound overwhelming powers, Rihito should be able to defeat the enemy with ease. However, the enemy, a group of trained and determined soldiers, will not go down without resistance.
The time travelers return to the future, and learn the true history of their world. Though they were unable to change the past, they are determined to correct the present and shape the future.
Nana throws a party for the weary time travelers after their long journey through history. One by one, they recover from the gloomy atmosphere brought on by what they had witnessed.
After Nana’s party, Hina confronts Licht as he is about to take off on his own again. As Schmerman’s Special Service Unit pursues its own mysterious goals, Alex contemplates his next move.
Licht takes off on his own and faces off against Doan, whose power completely overwhelms him. The others chase after him, while Jail visits his adopted father to seek closure.
Like he did in the past, Licht returns to life from what apparent death, and returns to save the others from Doan. However, Mizuka joins Doan. Licht must take both Aces on at once.
With Mizuka subdued, the only opposition facing Licht is Doan. Doan traps Licht in a prison of gravity, from which there is no escape. Hina, however, still believes in Licht.
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