Ash and company arrive at the Pokémon Center, but Nurse Joy is nowhere to be found. Pikachu inspects the room where she was and suddenly falls asleep. Ash follows it and meets the same fate. Outside, Team Rocket is knocked out of their tree by the gust from a Shiftry who is carrying away Nurse Joy. They decide they should capture it for their boss.
Back at the Pokémon Center, Ash, Brock, May, and Max are inspecting surveillance tapes to figure out why Nurse Joy is gone and why there is Sleep Powder in the room. They see the Shiftry taking Nurse Joy and decide to track it. They believe it is heading towards the largest tree in the forest. On their way, a number of Pokémon try to prevent their passage. Joy wakes up inside the top of the tree and is led to an ailing Nuzleaf.
At this point Ash and the gang arrive at the tree and start to battle with Shiftry and the other Grass-type Pokémon. Brock, Max, and May head for the tree and find Joy, who explains that she doesn't need rescuing. Team Rocket tries to steal the Shiftry, but it sends them blasting off again. By morning, Nurse Joy heals the sick Nuzleaf and Ash and his friends set off again on their journey.
While cutting through the mountains on their way to Mauville City, Ash and his friends decide to stop at a nearby Pokémon Center to rest for a while. Upon their arrival, however, they're met with an empty building; Nurse Joy is absent, and there's no sign of anyone else. All of a sudden, Pikachu's ears perk up and it leaps from Ash's shoulder and bolts up the stairs to the second floor. The group follows Pikachu, turning into the first room they find, gasping at the sight; Papers lay strewn across the floor, slightly blown by the breeze coming from the open window, and on the left side of the room lay Ash's unconscious Pokémon. While Max makes the assumption that someone may have broken in, Ash rushes to his partner's side, soon mysteriously falling unconscious as well. Meanwhile, somewhere out in the forest nearby, Team Rocket is laying within the leafy confines of a tree, enjoying the slight breeze as they soak in the sun. Their peace is soon disturbed, however, as a passing Shiftry flies by, bringing with it a gale that knocks the unsuspecting villains from their branch. They manage to spot the Pokémon before it disappears, planning on capturing it as a present for their Boss.
Back at the Pokémon Center, Brock manages to wake both Ash and Pikachu. He then notices a bit of powder on the Electric-type's nose and, after careful examination, recognizes it to be Stun Spore. Concurrently, Max notices a security camera mounted over the door and suggests they check out the tapes. Through watching said tapes, the group learns that a Shiftry invaded Nurse Joy's room through the window, knocked her out using Stun Spore, and took her away. Ash checks his Pokédex and gains the useful knowledge that Shiftry are "said to live in the tops of trees that are over 1,000 years old." Something seems to dawn on Pikachu and it heads for the window, calling the others over. As they gaze out over the forest, they spot a large tree that stood above all of the others; It was decided they would start there. As the four neared the tree, a group of Oddish jumped out from the bushes and attacked with Stun Spore, but it was easily blown away with a Gust attack from May's Beautifly. The Oddish retreated. As they proceeded even closer, the group was once again attacked, this time by a bunch of Seedot using Bullet Seed. May sends out her Torchic, scaring the grass Pokémon away with a super effective Ember attack. The four of them continue on, Team Rocket following closely behind. Next, they're jumped by a few Nuzleaf, which attempt to scare them away with Bullet Seed, but instead are driven into the trees by Ash's Taillow's Wing Attack. He recalls the bird Pokémon and they continue on their way, rushing faster than ever.
By this time, Shiftry has already arrived at the tree with Nurse Joy in hand, and he gently sets her down on a slab of wood. It isn't long before she wakes up, and at first, she is frightened of the Pokémon. All at once, a gigantic horde of Oddish, Seedot and Nuzleaf rush into the room, surprising her. She then inquires as to why she was brought here, and the Pokémon part, a lone Seedot emerging from the group. It calls out to her, beckoning her to follow. She does, and it leads her to a Nuzleaf, who appears to be unconscious and under a severe fever. Suddenly, a rather flustered Nuzleaf enters the room and yells something to Shiftry, who jumps from the tree in rage. Meanwhile, Ash and the group have nearly reached the tree. However, Pikachu suddenly stops and assumes a battle stance as Shiftry appears before them, looking extremely angry. Ash sends out Treecko, who rushes into a speedy Quick Attack, but Shiftry easily dodges it. The attack is returned with Shiftry's powerful Bullet Seed, which Treecko barely manages to dodge using a series of back handsprings. Ash tells Brock, Max, May and Pikachu to head to the tree while he subdues Shiftry. They agree and head off, Pikachu doing away with a few Nuzleaf using Thunderbolt along the way. Treecko and Shiftry exchange a few equal blows before they're stopped by Team Rocket's sudden appearance. They proclaim that they'll be taking Shiftry right then and there.
Back inside the tree, Nurse Joy is busy taking care of Nuzleaf when May, Max, Brock and Pikachu arrive. They notice the sick Nuzleaf and realize that Shiftry only brought Nurse Joy there to help it. They explain that Shiftry is fighting with Ash, and she asks the group to help her treat Nuzleaf and afterwards take her to Shiftry. They agree. Outside, Shiftry is still battling Ash and Team Rocket. With a Whirlwind and Bullet Seed attack, Ash's Treecko is thrown to the ground and nearly knocked out. It then blows Team Rocket away with another Gust. Nurse Joy appears soon after and tells Shiftry that there's no need to fight. She assures it that she'll take good care of Nuzleaf, but she needs to go back to the Pokémon Center to get some supplies. Ash comments on how far away it is, but Brock has an idea. He asks Shiftry if it can take him back to the Pokémon Center, and the Pokémon agrees, grabbing the unsuspecting Pokémon Breeder and zooming off into the forest with incredible speed. After the treatment with Nuzleaf is completed, it wakes up, and Nurse Joy proclaims that it will be just fine. The group then takes Nurse Joy back to the Pokémon Center after being thanked by Shiftry and the other Pokémon. After they say their farewells, Ash and his friends continue on towards Mauville City.