A direct sequel to the television anime's second season, The Golden City of the Scorching Sun, the film follows the young cave raider Riko, her robot companion Reg, and their friend Nanachi as they prepare to venture into the unknown depths of the seventh layer of the Abyss. Having resolved the conflicts of the sixth layer and helped the princess of the hollows, Faputa, fulfill her destiny, the group invites her to join their party as they continue their quest toward the bottom of the chasm. Their new destination is the Final Maelstrom, the deepest known layer of the Abyss, a territory shrouded in rumor and mystery, spoken of only in the oral traditions of the legendary White Whistle cave raiders.

The story takes place in the world of the Abyss, a colossal and inexplicable pit filled with the ruins of an ancient civilization, strange and dangerous creatures, and priceless relics. The descent is made perilous by the Curse of the Abyss, a deadly phenomenon that inflicts physical and psychological harm on anyone who attempts to ascend toward the surface, with effects ranging from mild nausea in the upper layers to certain death or the loss of one's humanity in the deepest zones. Riko, an orphaned girl living in the orphanage of the town of Orth on the edge of the Abyss, is driven by her desire to find her mother, the legendary explorer Lyza the Annihilator. Accompanying her is Reg, a mysterious amnesiac robot who possesses incredible strength and powerful weapons from his arms, and Nanachi, a tragic being who was transformed into a rabbit-like form by the Abyss's curse and possesses expert knowledge of the deeper layers. Now joined by Faputa, a powerful entity born from a desperate wish who is known as the "Princess of the Hollows," the group is united in their goal to reach the bottom of the netherworld. The movie is the first installment of a planned trilogy of films that will continue the story of the manga by Akihito Tsukushi.