Sacha and his fellow Pokémon trainers Max, May, and Brock become stranded in a desolate region, suffering intense thirst until aided by the Marina Group, a traveling circus showcasing Water-type Pokémon. With their help, Sacha learns of the People of the Water and their legendary Sea Temple, Samiya. They encounter Pokémon Ranger Jack Walker, who protects a Manaphy egg from the pirate Phantom. After Phantom attacks the Marina Group, Sacha and his friends join Walker's mission to deliver the egg to Samiya.

When Manaphy hatches and bonds with May, Sacha supports their connection. After Manaphy retrieves May's bandana and locates Samiya during a lunar eclipse, Sacha explores the undersea temple aboard a submarine piloted by the Marina Group's Lizabeth.

Inside Samiya, Phantom triggers flooding by removing crystals from the Sea Crown. Sacha helps restore the crystals to stabilize the temple. Finding the last crystal missing, he locates it in a fountain. Sacha places Pikachu, May, and Manaphy into an air capsule before swimming into the flooded chamber to reconnect the final crystal, causing Samiya to rise to the surface.

Surrounded by a glowing aura from the Sea Crown, Sacha pursues Phantom to rescue the kidnapped Manaphy. He then joins the counterattack against Phantom's ship alongside Manaphy and wild Water-type Pokémon. Following Manaphy's safe delivery to Samiya and May's farewell, Sacha and his friends depart from Walker and the Marina Group to continue their journey.