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.
On their way to Lake Valor, site of the Sinnoh Grand Festival, Ash and Dawn are practicing for their upcoming challenges, while Brock is preparing a meal. Dawn starts off with having Piplup use Whirlpool. She then praises Piplup for its Whirlpool. Brock is kneeling by a river preparing to clean some Berries when he sees a boat floating down the river with a girl fast asleep inside. As he attempts to wake her while walking alongside the boat, he realizes that it is headed straight for a huge waterfall. He starts yelling at her to try and wake her, but to no avail. He then wades into the water, grabs the boat, and blocks it from falling.
Brock is a couple of feet before the waterfall when he notices that there is a rope in the boat. He calls out Happiny, who proceeds to toss the entire boat and Brock onto the shore. Ash and Dawn come running up asking if he is okay. He says that he is and directs their attention to the girl, who suddenly opens her eyes and gets up. She asks about her basket, which is still in the boat with her. She then notices Brock and asks why he is all wet. Ash tells her that she was about to go over a waterfall. Dawn becomes agitated by the girl's passive attitude and tells her that she should thank Brock for saving her, but Brock shrugs it off. The girl exits the boat, introduces herself as Marley, and asks Dawn and Ash who they are. Ash and Dawn are taken aback by this and quickly introduce themselves and their Pokémon. Brock asks Marley why she was sleeping in the boat; she tells them that she was hiding and had accidentally fallen asleep. She also explains that there was a group of "very bad people" after her. She then turns to Brock and asks him to protect her while she goes to the other side of Mt. Coronet. Ash and Dawn interject by saying that she cannot just expect them to just say yes and bring her over the mountain. However, she responds that she wasn't asking them, angering Ash.
Brock eventually agrees to the offer, much to Ash and Dawn's distress. As the four are walking along a trail, Brock asks Marley where she will be heading after crossing over the mountain, and she says that she is headed to a very secret garden. Piplup's stomach soon starts to growl, so Brock starts getting out Pokémon food. Marley stresses how she was in a hurry and is reassured by Brock that it will not take long. Marley watches Piplup and Pikachu happily eating before she suddenly announces that she is going for a walk, surprising everyone.
Meanwhile, Marley opens her picnic basket and lets out a dirty, injured Shaymin, which she unsuccessfully tries to feed. Eventually, the others search for her and find her with Shaymin. Brock comments on how weak Shaymin looks and Marley says that it has been that way since the morning. When Brock examines it, Shaymin coughs up gas. Brock informs Marley that Shaymin has been exposed to a poison of some kind. Brock then explains how Shaymin can use a move called Seed Flare. Marley then recalls Shaymin inhaling a Seviper's Haze earlier that morning. Brock feeds Shaymin a Pecha Berry to rid it of the poison. Shaymin coughs up smoke and then explodes in a huge plume of black smoke. When the smoke clears, Shaymin looks completely healed. Brock then feeds it a Sitrus Berry to help it regain strength. After eating, it jumps up and utters a cry of happiness. Marley comments on how Brock is almost like Nurse Joy. Ash tells Marley that Brock wants to be the world's best Pokémon breeder. Dawn asks Marley why she keeps Shaymin in a picnic basket, and Marley says it was because the "bad people" are after Shaymin.
It is soon revealed that Team Rocket are the ones after Shaymin. They were walking along a path when Meowth spotted Shaymin. The trio immediately decided to capture it due to its rarity, but Shaymin escaped and encountered Marley. When the trio confronted Marley, they started reciting their motto, but she and Shaymin slipped away while they were distracted. However, they were quickly found, prompting Marley to send out her Arcanine, which used Flamethrower on Team Rocket and sent them blasting off.
Meanwhile, Marley tells the others about the time she tried to release Shaymin soon after the encounter with Team Rocket. However, it returned to her during the night, and she then decided to accompany it to the Gracidea Flower Garden, where she assumed Shaymin was naturally headed to. The next day, they were ambushed by Team Rocket, and Jessie sent out her Seviper, which used Haze. Shaymin started to suck all of the smoke into its body and used Seed Flare, giving it and Marley enough time to find shelter on the boat Brock found them in. As Ash and Dawn promise to protect her and Shaymin from harm, they come up to a tunnel. Marley announces that the Gracidea Garden is just beyond the tunnel. As they walk through the tunnel, Pikachu and Piplup trip on a sleeping Shroomish, which uses Poison Powder on them. Shaymin sucks the poisonous smoke in with Seed Flare and then releases it, scaring off the Shroomish. It then heals the poisoned Piplup and Pikachu with Aromatherapy. Marley later points out that they are almost at the end of the tunnel, and that there will be a huge Gracidea Flower Garden at the other end.
When the gang reaches the Garden, they realize that all of the Gracidea flowers have died. Ash suggests combing the dead garden in search of one that is still in bloom. Eventually, Brock sees a sprout, but it is on a huge rock. Team Rocket then bursts out in their giant Mecha Caterpie, which uses a String Shot. Ash commands Pikachu to use Thunderbolt and Dawn has Piplup use Bubble Beam against it; the attacks collide and explode in midair. Immediately afterwards, Ash brings out Torterra and has it use Energy Ball, which knocks Team Rocket down. As Team Rocket's robot starts crawling towards the gang, Brock suggests having Buneary use Ice Beam underneath Team Rocket, so that they have no traction. When that is done, and Team Rocket is immobilized, Ash has Torterra use Rock Climb and Dawn has Piplup use Whirlpool. The attacks land dead center and send Team Rocket spinning away. In response, Meowth engages the mecha's second stage, a Butterfree mecha. They begin charging a "Robo-Hyper Solar Beam", which they shoot at the ground, knocking Ash and his friends off their feet.
After the smoke clears, Marley looks for Shaymin, who she cannot find, but Brock points out that it is climbing the rock so it can get to the Gracidea and transform into Sky Forme. Meanwhile, Team Rocket dodges Pikachu and Piplup's attacks again and then starts charging another Solar Beam. However, Shaymin reaches the Gracidea and is exposed to its pollen, triggering its transformation. Once it is done, Shaymin jumps into Marley's arms for a quick hug, then flies through the antennae of the mecha Butterfree, cutting them to shreds. The trio then pursues Shaymin, but it is too fast for them. Team Rocket then uses "Robo-Hyper Gust", which knocks Shaymin off course, but it recovers and uses Air Slash, which cuts the mecha in half and sends Team Rocket blasting off again. Exhausted, Shaymin falls into the patch of ice created by Buneary and transforms back into Land Forme. As the gang wonders what to do next, two more Shaymin appear, and a Gracidea bud magically blooms right in front of them, so the Shaymin use it to transform. Once transformed, they take to the skies and fly in circles. Marley tells Shaymin that it was time for it to go on the Flower Bearing Journey. Though reluctant, Shaymin agrees, and Marley says that she hopes to see Shaymin again. Shaymin promptly flies away with its friends, but not without revealing its voice to thank Marley.