While doing some training in the forest, our heroes come across a mysterious girl sleeping in a boat...that's about to go over a waterfall! Fortunately, Brock acts quickly and dives in to save her. Once safe, she asks Brock to take her over the mountain, where she needs to find a "secret garden."

Although the girl, named Marley, is secretive at first, she opens up enough to explain that she is caring for a sick Shaymin. It turns out that Shaymin has ingested some poison from a Seviper attack, but not just any Seviper—Team Rocket's Seviper! They had been trying to steal Shaymin from Marley since the previous evening, and have shown up today to try again. Team Rocket makes a third attempt to steal Shaymin, but our heroes—and Marley—finally send them blasting off in their usual style.

Marley has been trying to get Shaymin to transform into Sky Forme, allowing the Pokémon to go on its flower-bearing journey. Up until now, Shaymin has preferred to stay with her. After finding one of the last remaining blooming Gracidea flowers in the field, Shaymin finally attains Sky Forme. The now-winged Pokémon, joining with two other Shaymin in Sky Forme, bids a fond farewell to Marley and our heroes.