Born from a cocoon in the village of Old Home, a young Haibane—a being with a halo and small gray wings—awakens to a world she does not understand without memories of her past. Named Rakka for the dream of falling she had while inside the cocoon, she soon becomes accustomed to life in the strange town. However, there are strict rules for the Haibane, such as being forbidden to leave the village or go near the walls surrounding it. These, along with mysterious disappearances of their kind on their Day of Flight, begin to unsettle Rakka and the others since they know almost nothing about their own kind. As Rakka and the other Haibane live their lives with no memories of the past, they try to break free from their former pain and ultimately find salvation.

Humans have enjoyed their lavish, peaceful, and prosperous lives for seven years since the day the almighty Spiral King was defeated—the day they reclaimed their homeland, Earth. However, the boon of this lifestyle leaves them unprepared when an unknown, hostile threat arises due to the ever-growing human population. This calamity is the Anti-Spiral—a fearsome enemy with unparalleled power. As the Spiral King's prognosis postulating the destruction of The Spiral's World begins to come true, the pieces are in place, and Team Dai-Gurren is ready. With his late brother's hope to see a better future for mankind, Simon—along with Nia Teppelin and the rest of the team—is determined to overthrow the mighty Anti-Spiral in order to revive humanity's lost hope.

Demons have now become commonplace around the kingdom of Midland, which has fallen into chaos. The swordsman Guts still cannot stay in one place for long due to his demonic brand. He could always manage to protect himself when he was alone, but now he has the added challenge of protecting former Commander Casca, a shell of her former self who neither remembers nor trusts him. They never have a moment's rest with the constant threat of demons, and they need a place where Casca will be safe till they find a way to heal her. Their elf ally, Puck, tells of the mystical land of Elfhelm, which is supposed to be a safe haven from the demons that ravage the lands. Tired and with only a vague hope, they struggle on to find a place to live—and they still need to find those responsible for the madness they are forced to endure.

An apocalyptic event has ravaged Japan, leaving nothing but endless sandy plains behind, and a strange rusting disease terrorizes the remnants of civilization. According to the government, the horrific state of the new world is the result of mushroom spores being spread by the likes of Bisco Akaboshi, labeled the Man-Eating Mushroom. But Bisco would beg to differ. In reality, he is a Mushroom Protector, determined to uncover the legendary Sabikui mushroom—said to be the ultimate cure for the rusting disease. Joining him on his quest are his giant crab Akutagawa and the kind doctor Milo Nekoyanagi, who is actively searching for a rust poisoning treatment for his sick sister. Despite the prejudice aimed toward him by the common folk, Bisco refuses to give up on his quest to purify the rotting world.