The story begins with the player moving to Alola and starting their journey as a Pokémon trainer, participating in the Island Challenge instead of the traditional gyms. As they explore the four islands, they face Totem Pokémon, Captains, and Kahunas, while meeting new characters such as the Ultra Recon Squad, who come from another world. The plot focuses on Necrozma, a mysterious Pokémon that threatens to destroy the balance of light in the world, and the player is called upon to stop it through travels in Ultra Wormholes and alternate dimensions.