Made in Abyss unfolds around the Abyss, a gaping chasm that plunges deep into the earth and teems with mysterious creatures and relics from a time long past. No one knows how it came to be or what lies at the bottom, and countless brave individuals known as Divers have descended into its darkest realms to solve those mysteries. The best and bravest of them, the White Whistles, are revered as legends by the people who remain on the surface.
Riko, the daughter of the missing White Whistle Lyza the Annihilator, dreams of becoming like her mother and exploring the furthest reaches of the Abyss. She is only a novice Red Whistle permitted to roam its uppermost layer when she has a chance encounter with a mysterious robot who looks like an ordinary young boy. She names him Reg, but he has no recollection of the events before his discovery. Convinced that the technology used to create Reg must have come from deep within the Abyss, Riko and Reg venture into the chasm to recover his memories and see the bottom of the great pit with their own eyes.
As their descent continues, the story expands beyond a single expedition into a larger portrait of the Abyss and the people shaped by it. Figures such as Ouzen, Nanachi, and Bondrewd reveal different sides of its allure and cruelty, while Riko and Reg press on through a world where wonder, loss, and danger are inseparable from the search for Lyza and the truth waiting in the depths.