Pikachu accompanies Ash Ketchum during their time in Alto Mare. Riding on Ash's shoulder during the Tour de Alto Mare water chariot race, Pikachu stays with Ash even after he falls off the chariot during a sharp turn. An invisible Latias later assists Ash and Totodile, providing a temporary speed boost; Pikachu shows no visible reaction to this intervention.

At a city water pump, Pikachu drinks when a girl activates it. This girl, later revealed as Latias in disguise, stares intensely at Ash before fleeing. Pikachu senses trouble when Annie and Oakley ambush the disguised Latias, prompting Ash to intervene. After Ash is injured by Annie's Espeon's Psybeam, Pikachu counters with Thunderbolt, forcing the attackers to retreat.

Pikachu follows Ash and the disguised Latias through Alto Mare's alleyways to the central piazza fountain, where the girl vanishes. Inside the museum, Pikachu stays with Brock and Misty as Lorenzo details Alto Mare's history and its Defense Mechanism.

Accompanying Ash into the Secret Garden after the disguised Latias reveals a hidden entrance, Pikachu is attacked by an invisible Latios and knocked backward. Following intervention by the real Bianca and Lorenzo, Latios licks Pikachu's face in apology, and the two Pokémon start playing together. Pikachu interacts peacefully with both Latias and Latios during this encounter.

When Annie and Oakley steal the Soul Dew and capture Latios, the escaped Latias seeks Ash's aid. Pikachu joins Ash and Latias racing through the gridlocked city to reach the museum and halt the malfunctioning Defense Mechanism. Pikachu remains beside Ash during the ensuing confrontation involving revived fossil Pokémon and the threat of a tidal wave.

Throughout these events, Pikachu travels outside its Poké Ball, typically perched on Ash's shoulder or walking beside him, communicating through vocalizations like "Pika" and "Pikachu." Its actions reflect loyalty to Ash, alertness to threats, and a capacity for playful interaction with other Pokémon.