This story begins with Ash and his friends heading for the Cinnabar Gym. Ash's path is not easy as he has to battle other Trainers along the way. When walking along, he comes across a Hiker that challenges him to a battle. The Trainer sends out a Rhyhorn while Ash counters with Bulbasaur. Rhyhorn executes a Take Down attack. The ground shakes as it charges right at Ash's Bulbasaur. Pikachu does not like this and puts on a look of desperation on his face. Ash commands his Bulbasaur to use Leech Seed, but Rhyhorn closes in and sends Bulbasaur flying before the attack is launched. Ash tries to recall Bulbasaur, but Bulbasaur refuses. Brock states that it will not back down until it wins and it seems that Bulbasaur really wants to battle it. The Hiker says Ash must be a bad Trainer if his own Pokémon does not listen to him and cannot even return it to its Poké Ball when told. Rhyhorn charges again, but Bulbasaur uses Razor Leaf, stopping it dead in its tracks before following up with a Vine Whip. Rhyhorn collapses and Ash wins. The Hiker commends Ash for training Bulbasaur well. Ash then notices that his Bulbasaur cannot get up, its bulb pulsating a blue glow.
They rush Bulbasaur to the nearest Pokémon Center. Ash tells Nurse Joy about what happened and asks her to save it. Nurse Joy hooks up Bulbasaur to a machine and runs some tests. Afterward, she returns to Ash and informs him that Bulbasaur is not sick at all. It is almost ready to evolve! Ash is purely excited, but Bulbasaur overhears Ash, not appearing to be as happy. Nurse Joy tells Ash that it will evolve at a special festival for Bulbasaur.
Everyone is asleep at the Pokémon Center and a long line of Bulbasaur goes past. Ash's Bulbasaur gets up and follows them. Pikachu sees this and decides that he will investigate. He wakes up Ash and they decide to follow him.
Jessie and James show up and Jessie sees all the beautiful flowers, enjoying them. James disagrees as he has allergies. Suddenly, they walk right past the big group of Bulbasaur holding Ash's Bulbasaur. Jessie says they should capture them, but the Bulbasaur all hit them with their vines, and they blast off again.
They are all following Pikachu. Brock says if they follow the trail of pollen, they might find Ash's Bulbasaur. Suddenly, the roots of a bunch of tree start thrashing around. A bunch of vines starts blocking their path to try to stop them from getting through. Ash says they will not stop, and they dive through them just in time. They were inside the Great Mysterious Garden, the legend was true, Inside are thousands of Bulbasaur.
Suddenly a tree starts to open and a Venusaur appears. It climbs on a big tree stump. Ash then scans it on his Pokédex. Brock comments on the description, saying that it makes it sound like a plant.
The gang searches for Ash's Bulbasaur; when they realize it has a bandage on its head, they manage to spot it. Team Rocket cannot get through the wall of vines. James asks Meowth to scratch his way through, and Meowth says he just had his claws filed. Jessie and James get out an axe and a saw. However, the vines attack them, and chase them away. Ash tries to yell out to his Bulbasaur; Brock stops him and reminds him that humans have never been in this garden before. All of the Bulbasaur are happy except for Ash's. All of the bulbs on the Bulbasaur's backs begin to glow.
The Bulbasaur start to evolve into Ivysaur one by one. Brock says that people have always disagreed whether Bulbasaur is a plant or animal. He says that maybe Bulbasaur are a symbol that all life on Earth is connected. Ash points out that his Bulbasaur is struggling to not evolve. The Venusaur yells at it, and all the Ivysaur start getting mad. The Venusaur is about to hit Bulbasaur with its Vine Whip, but Ash blocks it just in time.
Ash apologizes for coming to their festival, but states Bulbasaur is his friend. He asks if they are mad that Bulbasaur will not evolve, and they all nod. Ash says that if Bulbasaur does not want to evolve, they cannot force it to. A bunch of pollen comes from the flower on Venusaur's back and goes on the tree, causing it to grow more. Misty says that it's manipulating nature. Venusaur says to Bulbasaur that if it evolves, it could do that too. It still refuses to evolve.
Team Rocket arrives in their balloon. All of a sudden, they start sucking up the Ivysaur into a bag. Pikachu flies up and Ash's Bulbasaur catches it with its vine. Ash tells Bulbasaur to knock Team Rocket out of the sky. Bulbasaur tries using Razor Leaf, but it fails. James asks if they should get Bulbasaur, and Jessie and Meowth just laugh, saying Bulbasaur is a wimp. Bulbasaur shouts and the sun suddenly rises over the horizon. The sun's rays enters through the opening into the top of the bulb in Bulbasaur's back. The Pokédex says it's getting ready to use Solar Beam. Ash tells it to ready its Solar Beam. The bulb glows, and a huge, blue beam of energy shoots out, hitting the balloon. The balloon explodes, and Bulbasaur frees all the Ivysaur with Razor Leaf.
Team Rocket falls to the ground in the basket. All the Pokémon are mad. They hit Team Rocket at once with all their vines, and they go flying for the second time in one episode. Ash says Bulbasaur did great. Venusaur agrees, extending a vine. Bulbasaur extends its vine and connects with Venusaur as a sign of respect.
Ash and the others leave. They notice that the garden has disappeared. They wave goodbye to Venusaur and Ivysaur.