Hyakushiki Kaito is an exceptionally clever thief renowned for executing intricate tricks and escaping perilous situations. He rescued Lili Hamilton from a laboratory where her Scottish alchemist father conducted experiments, granting her psychic abilities to read minds and understand emotions. Following this rescue, Kaito became Lili's legal guardian; she affectionately calls him "Uncle."

Operating within the fictional town of Goshikichō, Kaito's actions intersect with the Yoshinaga family and their guardian gargoyle. His motivations center on protecting Lili from further exploitation and thwarting pursuers of the Philosopher's Stone, a legendary alchemical artifact tied to the gargoyle's origins. His expertise in deception and evasion makes him a strategic ally in conflicts against alchemists and adversaries seeking the stone.

Kaito's relationship with Lili evolves into a protective dynamic, providing stability after her trauma. This guardianship includes collaborative efforts, like when Lili temporarily assumed his phantom thief persona during his illness. While he interacts with others such as Futaba Yoshinaga and her friends, his primary focus remains ensuring Lili's safety.