[4][5] 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.

Once Pikachu awakens, he and Tim are visited by Mewtwo, who reveals that the recent uptick of Pokémon incidents is not caused by R, but from something else, as well as preparing to disclose intel on Harry.

The next day, Tim and Pikachu join Rachel to meet her professor, Trevor Gordon, at some mysterious ruins south from Ryme City, hoping to gain more information on the Aurora Drop.

After discovering that Gordon had entered the ruins two days prior and hasn't returned since, the three investigate the temple's puzzles and solve the mysterious riddles.

[6] A tie-in anime short, titled Detective Pikachu & the Mystery of the Missing Flan, from Polygon Pictures was released on YouTube on October 25, 2023.