Rei finds himself in a strange void and is sent back in time to Hisui by Arceus, who tasks him with seeking out all Pokémon and transforms his smartphone into the Arc Phone. A stranger to the land and wearing odd clothes, he meets Professor Laventon, who invites him to join the Galaxy Team Survey Corps of Jubilife Village as a way of obtaining food and shelter. The Survey Corps also wish to fill out the Pokédex, and so, after proving himself worthy, Rei is admitted into their ranks.
As part of his duties, he is commanded by Kamado to seek out the recently frenzied Noble Pokémon and quell their frenzy. After all of them are quelled, the rift in the sky that caused the frenzies expands even further. As such, Commander Kamado banishes Rei from Jubilife Village on suspicion. He meets with Cogita and the merchant Volo, and with their guidance seeks out the lake guardians to obtain the Red Chain. While the Chain fails to work as planned, Rei is still able to catch both Dialga and Palkia, one of which is caught with the Origin Ball crafted from the Red Chain, causing the rift to disappear.
Afterwards, Rei collects the Plates with Volo and Cogita's help. Once 17 of the 18 Plates have been collected, Rei meets with Volo atop Mount Coronet, where it is revealed that Volo's consorting with Giratina was the cause of the rift. He attacks Rei in an attempt to take the Plates for himself. After being defeated, he gives Rei the final Plate, the Spooky Plate, allowing Rei to obtain the Azure Flute.
Once Rei has completed the Pokédex, he returns to the summit of Mount Coronet and plays the Azure Flute, revealing a glowing stairway that leads him to the Hall of Origin, where Arceus challenges him. After being defeated, Arceus grants Rei a fragment of itself and the Legend Plate.
As a non-playable character
Rei works as Professor Laventon's assistant, helping to teach the player how to catch Pokémon and how crafting works. Each time the player completes a mission, he joins the Professor and the player for some potato mochi. During the game's climax, he assists the Professor in crafting the Origin Ball.