The story follows a boy named Quon and others who suddenly wake up with supernatural powers.

After fending off the threat of a Neuroi invasion of Romagna and destroying the enemy's nest over Venezia, Yoshika Miyafuji goes back to her home town in the Empire of Fusou. Despite the loss of her magical and healing abilities, the former officer of the 501st Joint Fighter Wing wants to continue studying medicine. This is in order to help those in need, both civilians and those on the front lines alike. She receives an invitation from a prestigious school in Europe and decides to accept the offer, embarking on a journey back to the war-torn continent. However, a new danger arises, as more and more Neuroi manage to break through human defense lines, appearing unnoticed in supposedly safe areas and disturbing the balance of power in Europe. Yoshiki's sense of duty collides with her inability to pilot a Striker Unit, but with her friends in peril, it seems that there is only one thing she can do.

Denizens from the Crimson Realm continue to infiltrate Misaki City and steal life energy from humans. To combat this threat, Flame Hazes are tasked with saving humans from losing their existences. But while it is a Flame Haze's duty to protect humans, Shana—the "Flame-Haired Burning-Eyed Hunter"—seems to be focusing her attention on one human in particular: Yuuji Sakai, a teenage boy who was unwittingly dragged into the fight between Crimson Denizens and Flame Hazes. Since her first encounter with Yuuji, Shana has started to see him as more than just a friend. In fact, Yuuji wonders if Shana might have revealed her feelings to him once before, but it is difficult for him to confirm due to her hot-and-cold personality. Nonetheless, their days pass like any other, until a new transfer student arrives at their high school—one who bears a striking resemblance to an old enemy. Yuuji and Shana have no time to dance around their feelings for each other; while their adversaries from the Bal Masqué organization plan their next attack, the two must keep their guard up as they explore the origin behind the coveted magical object within Yuuji's body, the "Midnight Lost Child." [Written by MAL Rewrite]

Naho Takamiya's first day of her sophomore year of high school is off to an uneasy start. After waking up late, she receives a strange letter addressed to her. However, the letter is from herself—10 years in the future! At first, Naho is skeptical of the note; yet, after witnessing several events described to take place, she realizes the letter really is from her 26-year-old self. The note details that Naho's future life is filled with regrets, and she hopes that her younger self can correct the mistakes that were made in the past. The letter also warns her to keep a close eye on the new transfer student, Kakeru Naruse. Naho must be especially careful in making decisions involving him, as Kakeru is not around in the future. With the letter as her guide, Naho now has the power to protect Kakeru before she comes to regret it once more. [Written by MAL Rewrite]