The story follows an orphaned young girl, Riko, who finds and befriends a humanoid robot Reg and descends with it into the titular "Abyss", that leads deep into the Earth, in hopes of finding her ...

"No one has ventured into the sixth layer of the Abyss and remained unchanged. Even with the possession of a White Whistle, an ominous specter hovers above Riko, Reg and Nanachi as they advance ...

After the events of Made in Abyss: Dawn of the Deep Soul, Riko, Reg, and Nanachi enter the weird bubble ship and descend through a deep ocean into a sunny land--the titular "land of the scorching sun.