Two years after Tim Goodman and Detective Pikachu solved the case behind the R incidents, and in the midst of their search for Tim's missing father, Harry, they are invited to be awarded medals for their continued detective work by Ryme City's mayor, Martin Myers, who hopes to initiate the inaugural Pokémon Friendship Week to redefine the harmony and coexistence between humans and Pokémon, following a recent rise in Pokémon-related incidents. However, a frenzied Corviknight interrupts the ceremony. After the two briefly help a wild Pidove knocked out from the chaos, they are called by Inspector Holiday to investigate the theft of a priceless jewel, the Aurora Drop, at an estate owned by jeweler Sanjeev Denis.
At the Denis estate, the Ryme City police accuse Sanjeev's trusted friend and butler Brandon Barnes as a suspect. Believing Barnes has an alibi, Tim and Pikachu investigate, and with some help from Sanjeev's Growlithe, Tim exposes the recent hire, Larry Turner, as the culprit, proven by a note written by him that reveals his plan to frame Barnes, hiding the stolen jewel in the belly of his Pokémon, a Cramorant. However, upon Pikachu noticing a strange device on Cramorant's back, it swallows the jewel and flies away, with Turner denying any further involvement.