In Orth, a city at the edge of the Abyss lives the young Cave Raider in training, Riko. During an expedition, she discovers the unconscious robot boy, Reg.
The children try to find out more about Reg's origins and use Jiruo to keep him out of trouble. Riko gets to read her mother Lyza's letter.
A sentence in the letter inspires Riko to make the dangerous journey into the Abyss. Wanting to find out more about his origins, Reg joins her.
As Riko and Reg reach the first layer, they meet Habolg. He was asked by Nat and Shiggy to assist them. But Riko doesn't want his help.
Riko and Reg have arrived at the Forest of Temptation in the second layer. When a Corpse-Weeper abducts Riko, Reg fires his incinerator.
After Riko and Reg arrive at the Seeker Camp in the second layer, they are greeted by the White Whistle Ozen. She informs Riko that Lyza is dead.
Ozen seems to harbor resentment toward Riko. When Reg steps in, a fight breaks out between him and Ozen. Soon everyone gets involved.
Riko and Reg successfully complete their survival training. Before Ozen sends them on their way, she gives Riko Lyza's pickax that she found.
Riko and Reg descend through the Great Fault using a cave system to avoid the Madokajacks. Riko realizes, how important Reg is to her.
Riko and Reg continue traveling down through the Goblet of Giants. But as they get deeper, they feel a presence that seems to move all around them.
Nanachi brings Reg and the badly injured Riko to her hideout where she lives with another creature. Both used to be human before a curse changed them.
Back in Orth, Kiyui gets sick on his birthday. In the Abyss, Nanachi trains Reg who manages to drive off a monster. Nanachi asks Reg to kill Mitty.
Reg frees Mitty from her misery. After sending a message balloon to the surface, the three set out to leave the fourth layer.
A long time ago, an expedition group set sail in search of a legendary city said to be located within a massive abyss.
At long last, Riko, Reg and Nanachi make it to the sixth layer. Riko is fascinated by the strange creatures and structures they come across.
While searching for the White Whistle, the friends arrive in a mysterious village of sentient Hollows, where everything has a clear value.
A strange creature insists that Reg is her close friend, but Reg can't seem to remember who she is.
While trying to return to the village, Reg comes under attack. Riko searches for her friends in a mysterious cave.
Riko needs to free Nanachi, but the price she'll have to pay is too high; she'll have to give up both her eyes, legs or half her organs.
Many years ago, before the founding of the village, the explorers quickly realized that they are unable to leave and will have to remain here forever.
Thanks to an unexpected sacrifice, Reg may be able to save Nanachi. The dark, painful truth about the foundation of the village is finally revealed.
Reg rushes back to the village with the arm to save Nanachi, but he isn't sure if he can keep the promise he made.
Nanachi wakes up and wants to go in search of Reg and Riko. But if Nanachi wants to leave the village, they'll have to make a sacrifice.
Unfairly blamed for Reg's amnesia, Riko finds herself under attack — but then, an unlikely figure puts themselves in harm's way to save her.
Riko reflects on her decision to come to this village. As everything crumbles around them, the villagers are called upon for a final sacrifice.