Pikachu functions as Ash Ketchum's primary Pokémon partner throughout the film. As a species, Pikachu stores and discharges electricity through specialized cheek pouches, using its tail as a grounding rod to control electrical energy—a universal trait of its kind.

During the group's first encounter with the Marina Group's traveling water circus, Pikachu displays curiosity toward the performing Water-type Pokémon. It watches Meditite and Medicham employ Psychic abilities to manipulate water spheres holding Poliwag and Poliwhirl, revealing its fascination with novel Pokémon performances. Pikachu joins Ash and his companions inside the water spheres during the act, demonstrating adaptability in aquatic environments despite its Electric typing.

When the mercenary Phantom attacks to steal the Manaphy egg, Pikachu participates in defensive efforts alongside Ash and allies. Inside the sinking Sea Temple of Samiya, Pikachu accompanies Ash, May, and Manaphy into the flooded Crown Chamber. As water overwhelms the temple, Ash secures Pikachu, May, and Manaphy within an airtight escape capsule from Phantom’s submarine, isolating them from immediate peril during the temple’s restoration.

After Ash seemingly sacrifices himself to restore the Sea Crown, Pikachu shares a moment of intense grief with May near the temple structure. Phantom interrupts this by resurfacing to abduct Manaphy. Pikachu later witnesses Ash’s revival through the Sea Crown’s energy and contributes electrical attacks in the counteroffensive against Phantom. During this battle, Manaphy directs wild Water-type Pokémon—including Kyogre—to dismantle Phantom’s ship and subdue him.

The film ends with Pikachu traveling alongside Ash and friends as they depart the Marina Group and Jack Walker, continuing their journey after ensuring Manaphy’s safety as guardian of Samiya.