Ash, May and Brock show off their Pokémon to Professor Birch who compliments them all. The group begins walking toward a forest where they discover three Seedot that seem to be very unhappy. After Birch explains how to make friends with the Seedot, which involves rubbing them with leaves and rolling on the ground with them, the group tries to put the Seedot back into the trees. The trees seem to be too dry for the Seedot, so the gang decides to help them.
Meanwhile, Team Rocket is devising a plan to capture the Seedot. Jessie is gushing over how wonderful it's going to be when her Silcoon (which is actually a Cascoon) evolves into a Beautifly. James and Meowth shudder at the impending doom. Team Rocket meets up with the group and attacks them, trying to capture the Seedot. May then uses her Silcoon to attack Jessie's Cascoon. May's Silcoon then begins to glow and evolves into a Beautifly! May is overjoyed with her new Pokémon. Corphish sends Team Rocket blasting off again with its Crab Hammer attack.
Jessie vows to make her Cascoon evolve. After trying to pit it against their own Pokémon, Team Rocket hunts down Ash and company to challenge them again. Jessie attacks May's Beautifly with her Cascoon and it begins to glow. Meowth and James try to hide the newly evolved Dustox, but Jessie pushes them out of the way. She shocks everyone by being ecstatic by her new Dustox because she thinks is looks so much more powerful than Beautifly. After more fighting, Corphish send Team Rocket on their way again and Ash and the gang part ways with Professor Birch.
Ash and his friends are sitting at their camp with Professor Birch. Ash then lets out Treecko, Taillow, and Corphish to show the Professor the progress he's made. May decides to call out her Silcoon, and Brock releases Mudkip and Lotad. Birch admires them all, but when he gets to Brock's Pokémon, Lotad is facing the wrong way, so Mudkip turns it around. The group shares a few laughs as Lotad stares off into space. Meanwhile, somewhere out in the forest, Jessie is polishing her Cascoon while telling it what a beautiful "Silcoon" it is. James and Meowth try multiple times to tell her that it's actually a Cascoon, but she simply won't listen. James takes out a Pokémon card with Silcoon painted on it to show Jessie, but she ignorantly remarks that the card is wrong.
The group and Birch set off into the forest to find a new training location when they come across some seemingly unhappy Seedot hanging from a tree. After some observation, the Professor comes to the conclusion that the cause is due to the recent landslide nearby that took down their favorite trees to drink moisture from. He then suggests rubbing the Seedot with leaves to cheer them up, and Max is astounded that it actually works. After that, the Professor plays with the Seedot by rolling on the ground with them; this allows him to communicate and connect with the Pokémon at their own level. As Team Rocket observes Professor Birch playing with the Pokémon, they spin a devious plot to steal the three Seedot and give them to Giovanni as a present. All of a sudden, a Haze attack spills into the area, and Team Rocket appears from their hiding place. Ash sends out his Corphish and subdues Seviper with a Vice Grip attack. Jessie sends out her Cascoon, proclaiming it to be a Silcoon upon throwing the Poké Ball. Professor Birch quickly corrects her, adding that she actually has a Cascoon. May calls out her Silcoon to prove the Professor’s point, and Birch exclaims that Silcoon and Cascoon are notably different because of their eyes. Jessie insists her "Silcoon" will evolve into a Beautifly and she orders it to use Tackle. May calls on her Silcoon to do the same, and as the two Cocoon Pokémon Tackle each other, May's Silcoon evolves into a Beautifly. May is ecstatic about her new Pokémon and checks her Pokédex eagerly. Jessie, however, is determined to prove her “Silcoon” is still better and orders a String Shot. Though Corphish breaks the silky thread with its claw before sending Team Rocket off with a Crabhammer.
Afterwards, Beautifly lands on May's head. Brock then gives May a special food gel for Beautifly that he pre-prepared for the day Silcoon evolved. They discuss Beautifly's new moves and Professor Birch hands May a frisbee, telling her that if she wants to start winning Pokémon Contests, she will have to start working very hard. May then throws the frisbee, telling her Beautifly to keep it spinning in the air using its newly acquired Gust attack. Meanwhile, deep in the woods, Jessie forces Meowth to fight her Cascoon in order to raise its experience, so it'll evolve. Despite Cascoon successfully knocking Meowth out with its Tackle attack, it wasn't enough. Jessie then battles James's Cacnea, but after yet another victory with no result, Jessie decides that she needs to battle stronger Pokémon. She sets her sights on the nearby twerps.
Just after Ash and company find a flourishing tree that the Seedot like, Team Rocket appears, and Jessie challenges the group to a battle. May accepts and leads the attack with her Beautifly, sending Cascoon flying backwards with Gust. James sends out his Cacnea to help, while Ash calls out Treecko. Cacnea makes the first move, sending a Pin Missile attack Treecko's way, which it skillfully dodges. Treecko returns the favor with a Pound attack, narrowly missing Cacnea with its dangerous tail. Amidst the chaos, Meowth attempts to sneak around and kidnap the unsuspecting Seedot, but is stopped when Brock calls out Mudkip to use its Water Gun on him. During the battle between Jessie and May, Cascoon starts to evolve. Fearful of Jessie's wrath, Meowth dresses up as a Beautifly while James hides the newly evolved Pokémon. This is seen through easily, however, and Jessie uncovers it, only to find not a Beautifly, but a Dustox instead. Confused, she wonders how this is possible, considering that she had caught a Wurmple just like May, and both of them had evolved at the same time. Professor Birch explains to Jessie once more that her Pokémon was a Cascoon, not a Silcoon, so the only thing into which it could have evolved was a Dustox. This time, Jessie listens to him, and much to everyone’s surprise, she adores her new Dustox.
She becomes overconfident in her new Poison Moth Pokémon and challenges May's Beautifly. She first has James tell her Dustox’s move set, and she is impressed. The battle begins with a Tackle from Dustox, which hits Beautifly head-on, but the Butterfly Pokémon quickly regains its composure and returns the favor with a Tackle of its own. Jessie becomes enraged and commands Dustox to use Poison Sting, but it's easily blown away by Beautifly's Gust. James decides to join in and has Cacnea use Pin Missile while Dustox shoots a Psybeam, but Treecko leaps in front of Beautifly and takes both attacks. Ash recalls the brave Pokémon and sends out Corphish, who quickly jumps to avoid another Pin Missile from Cacnea. Beautifly dodges a Poison Sting from Dustox and slams it with a Tackle, sending it reeling into its Trainer, both of them hitting the ground. After Corphish deals with Cacnea using Crabhammer, it sends a Bubble Beam at their balloon, causing an explosion which sends them blasting off once again. Professor Birch and the others' attentions return to the Seedot, who are happily attached to a tree branch. Birch inspects the soil and declares that is appears to be nutrient rich. As the sun sets on the horizon, Professor Birch bids the group farewell before heading back to Littleroot Town.