On her way to school one day, Suzume Iwato stumbles upon Souta Munakata, a young man searching for abandoned areas. The high school girl directs Souta to a nearby ruin, but out of pure curiosity, she herself decides to head to the same destination. Once there, Suzume discovers an isolated door with a dreamlike universe lying beyond it—a place that she can see and feel, but not enter. A strange stone rests on the ground nearby, but it turns into a cat-like creature and scurries away when Suzume lifts it. Suddenly afraid, she heads back toward her school, not realizing that her act of leaving the door open will have consequences. With the "keystone" released, the evil within the other universe can now freely escape and wreak havoc throughout Japan. Intending to correct her dangerous mistake, Suzume joins Souta—whose true goal is to prevent evil from festering—in finding and locking all open doors before the country is destroyed.

The fifth season of FLCL, and sequel to FLCL: Grunge. The anime will take place 10 years after FLCL Alternative and will center on a high school boy and girl.

The story centers on Nayu, a middle school girl who shocks her schoolmates on the first day of school by wearing black lace panties. She likes this kind of underwear, and she tries to "spread the word on the merits of [these kinds of] underwear" via an underwear club with her schoolmates, who are worried about their bodies' development and which underwear to choose.

Lunia, the daughter of the Count of Persephone, was shunned by her father and treated like a tool by her half-brother, leading a lonely life. Meanwhile, she is chosen by a priest to be engaged to Hades, the head of the Duke of Khronoa family, and decides to marry into the cursed duke family. The Duke of Khronoa, feared as the "King of the Underworld," is cursed with a short lifespan if he does not marry a bride chosen by the emperor. However, Hades tells Lunia that he has no intention of loving her. In order to keep Hades alive, Lunia deceived him and spent the night with him, then disappeared without realizing that she was pregnant with his child. Seven years later, Hades somehow managed to find Lunia and tried to take her back with the child...