Nurse Joy inside a Pokémon Center does research, but notices that the wind is entering her room when the window is opened. She recalls closing it, but the wind gets very strong, with a creature stepping on the window and she scrams! The gang is traveling to Mauville City and they stop to the Pokémon Center. The gang enters, with Brock introducing himself already. However, she is not present and Pikachu smells something. Pikachu climbs the stairs, leading them to an empty room with papers lying around.
Ash spots Pikachu fallen and when he gets it, he falls down as well. Team Rocket enjoys the nature, but a Pokémon with Nurse Joy on it passes, surprising and making them fall down. Meowth identifies the Pokémon to be a Shiftry and begins to imagine his boss, Giovanni waking up in hot summer day, so if they were to capture Shiftry, the boss would cool down in that day. Brock wakes Ash and Pikachu and notices some blue powder on Pikachu's nose. Brock identifies the powder as Stun Spore. May spots that the computer in the room belongs to Nurse Joy.
Max notices the security camera, so they look when Nurse Joy disappeared. She has been kidnapped by the Shiftry. Shiftry used Stun Spore to make Nurse Joy asleep, making Brock super-furious that it kidnapped her and swears to get her back. Max knows that Shiftry can't use Stun Spore, while Pikachu spots the gigantic tree, making it the place where Shiftry went to. As the gang goes to save her, Oddish intercept them and use Stun Spore, but May's Beautifly uses Gust to blow the attack away. The Oddish have disappeared, so they advance. Shiftry has arrived inside the tree. Some red eyes appear in the woods and they go out - it are Seedot. Seedot attack the gang, but they run away in safety. The Oddish appear as well, standing to defend. Shiftry places Nurse Joy on an altar, while Seedot attack the gang.
Ash proposes to use Pikachu, but Max thinks Torchic should be sent instead, so she sends it. Torchic uses Ember, defeating the Pokémon. Team Rocket hides behind the woods, planning to steal Shiftry, even if the gang goes after it. Nurse Joy awakes and is scared of the Shiftry that appeared next to her. The gang has come to the river, but suddenly, rocks begin to explode, revealing some Nuzleaf! Nurse Joy attempts to escape, but cannot as she is too high to jump!
Ash, per Max's advice, sends Taillow and it uses Wing Attack. Nuzleaf go away, making the path safe. Max wonders if the Nuzleaf, Oddish and Seedot were waiting to ambush them, but Ash orders them to go to the tree. Team Rocket appears as well, loving the fact that the gang is destroying traps, making their job easier. Nurse Joy demands to know what the Shiftry wants, but suddenly the Nuzleaf, Seedot and Oddish appear, with the wind getting stronger, making her confused. Nurse Joy follows a Seadot and she sees a problem - a Nuzleaf is diseased, having high temperature. Another Nuzleaf appears, warning Shiftry of the gang approaching, so Shiftry runs to defeat them. The gang encounters Shiftry, so Ash sends Treecko - Treecko uses Quick Attack. However, Shiftry's speed makes him miss. Shiftry uses Bullet Seed, but Treecko evades the attack. Treecko uses Pound, but Shiftry dodges even that attack. The others go, leaving Ash to deal with it.
They are ambushed by Nuzleaf, but Pikachu uses Thunderbolt, defeating them. Treecko and Shiftry battle fiercely, but they are stopped when Team Rocket appears. Meanwhile, the rest of the gang have come to the tree and they climb up and see Nurse Joy tending the Nuzleaf. Brock comes to rescue, but Joy replies she isn't in danger. Nurse Joy wants them to help her, then to go to Shiftry to warn it. Shiftry blasts them off, with Jessie's Wobbuffet claping and having a rose in its mouth. Shiftry attacks Treecko, but he dodges. However, Shiftry jumps and uses Bullet Seed, hitting Treecko. Nurse Joy appears, warning Shiftry that it does not need to fight Treecko. Brock explaines to Ash that Nurse Joy was brought to the tree to take care of the Nuzleaf who got ill. Brock will get the supplies Nurse Joy needs to heal Nuzleaf, so he rides Shiftry since Pokémon Center is far away, although it has an amazing speed.
After some hours and treating, Nuzleaf is feeling much better. Everybody cheers and the Shiftry goes away. The next day, the gang leaves as well.