One day, Pikachu and its friends are walking along when they suddenly fall through a Diglett hole and into Pokémon Valley, a secret location that no one knows about. Pikachu and its buddies tell the Pokémon that they could use some help looking for Togepi, who fell through the hole first. The group sets off and eventually finds Togepi in the Exeggcute nest—but one of the Exeggcute is missing. That leads the group on another hunt; this time, though, Pikachu and its friends come back to the nest empty-handed. That’s when a storm begins to brew, filling Pokémon valley with roaring thunder and gusts of wind that almost blow the friends—and the Exeggcute nest—away! Are the friends going to be able to keep the nest safe and reunite the Exeggcute?
Ash and his friends are resting in a campsite, and all of their Pokémon are sleeping. A group of Ledyba flew by, waking Togepi. Togepi jumps up and watches them. Then Togepi yawns and falls back down a hill, waking Pikachu and the rest of the group's Pokémon. They, then going after Togepi and while exploring, find themselves lost. Togepi continues to roll down, hitting a lost Meowth on the way. They both fall down a tree stump. The group's Pokémon are calling for Togepi, but don't get a response. Psyduck then comes running down the hill and knocks Pikachu and the others down the tree stump. The tree stump leads off a mountain. Some Ledyba catch them just before they hit the ground. The Ledyba drop them off in some leaves. They then come face to face with an Elekid. It and Pikachu start to fight and Meowth is seen stuck on a tree branch. He screams for help, waking a Gyarados, who attacks, though Meowth escapes.
Back with the group, Pikachu and the rest follow Elekid to a tree, where Togepi can be seen with some Exeggcute. Pikachu runs up the tree, but the Exeggcute stop him. Bulbasaur then uses his vines to grab Togepi, but one of the Exeggcute bites his vine. Squirtle then notices that one egg is missing. It seems that they want Togepi to fill the spot. The group searches for the lost Exeggcute.
Bellossom make an appearance, putting on a show the group. When finished, the group meets some Clefairy, who use Metronome, which turns into Explosion. This blows a hole in the cave, throwing the gang in the air. Pikachu and Elekid both collide with Meowth. They fall onto a Snorlax, bouncing off it, and into Gyarados's waterfall. The trio have a fight over who gets to ride Gyarados. Pikachu uses Thunderbolt, causing Meowth to blast off. Pikachu and Elekid meet up with the rest of the group again. A storm begins to stir, almost forcing the Exeggcute out of the tree. The group, as well as many forest Pokémon, try to help the Exeggcute. Thunder brews, and a strike of lightning hits the tree, causing a fire. Squirtle and Marill put the fire out by using their Water Guns. The nest with Togepi in it then blows away. Bulbasaur uses his vines to catch the nest. Now, Bulbasaur start to blow away, so all the Pokémon create a chain to save him. Finally, the sun then comes out, and Dragonair flies across the rainbow, Pikachu grabs Togepi in happiness. The Exeggcute are still missing one of their eggs. A Chansey then returns the last egg that she'd been looking after. The Exeggcute jump around a Leaf Stone in joy, and while doing so they evolve into Exeggutor. The group says their farewells and return to their Trainers.
The "welcome song" that the Tree residents sing to Pikachu and his group when they arrive also played in the background of the main menu for the DVD of Pokémon the Movie 2000.
Although Exeggutor is usually described as having three heads, this is the first time an Exeggutor in the anime is confirmed to have only three heads, as all Exeggutorseenpreviously have had at least four to six heads.
The Butterfree seen are of the normal variation, rather than the Orange Islands variation.