The group finds themselves lost in Petalburg Woods, and a fight soon erupts between siblings May and Max. Brock manages to separate the pair, though tensions remain high. Ash suddenly sees a bunch of Treecko running through the trees. He says that he had wanted one since he first saw one at Professor Birch's lab. He quickly tosses a Poké Ball, but the Treecko bats it away with its tail, and May sarcastically reminds Ash that you have to battle the Pokémon first. Their talk is cut short when Brock notices that the Treecko are running away.
Ash chases after them and the others follow. Ash sees what looks like a huge, odd tree up ahead. Unfortunately, he doesn't pay attention to where he's going and falls face first down a steep hill. When he looks up, he sees that the tree is right in front of him, and it's massive. It's more than twice as tall as all the other trees in the forest. Ash comments that it looks almost magical, but he notices that it has no leaves and looks somewhat dead. Suddenly a sharp twig lands in the ground right in front of Ash's face. He looks up and sees an angry-looking Treecko sitting on a branch with another twig in its hand. Ash challenges the Treecko to a battle. Treecko leaps into action, jumping between the branches before spitting its twig at Pikachu. Pikachu dodges, but Treecko lands next to him and delivers a powerful whack with its tail. Treecko taunts Pikachu, urging him to attack. Pikachu rushes towards his opponent, though Treecko dodges and strikes Pikachu again with its tail.
Meanwhile, Team Rocket watch on and are mildly impressed with Treecko's reflexes. Meowth explains that Treecko would make a great masseur for Giovanni. The boss fantasy sets the Rocket trio's sights on capturing the Treecko for themselves. Ash and Pikachu soon find themselves surrounded by a large group of Treecko. An older Treecko attempts to talk to the one that Ash just battled, but is yelled at and pushed backwards. The other Treecko look pretty mad, but the old Treecko urges them not to attack. Jessie is excited because she loves watching other people's troubles, and asks Meowth for a translation. The old Treecko says that the tree is going to die and all the Treecko need to move to another tree. However the other Treecko remains defiant, replying that it was born on that tree and isn't going to give up on it, no matter what. The sentiment really moves James and Meowth, but Jessie doesn't think it's very heroic at all, since life is full of change. She explains all about this, until they notice that all the Treecko are leaving except for one. Once the others are out of sight, that Treecko rushes off too. Ash is prepared to follow it, but Pikachu has a better idea, so they stake out in the tree.
Brock has since cooked up a meal for him and the others to enjoy. Max is worried about Ash, but Brock assures him that Ash will be fine, and they agree to go look for him after they're done eating. As the sun sets, Ash and Pikachu are still waiting at the old tree. Ash decides to send Taillow to look for his friends, since he's afraid they might be worried about him. As soon as Taillow flies away, Treecko appears carrying a leaf full of water. It carefully waters the tree before placing some dry leaves down to keep the ground from drying up again. Treecko goes off to get more water, as Ash wonders whether it's too late to save the tree. As darkness falls, he and Pikachu start to help the Treecko water the tree. It's angry at first, but it warms up to them when it realizes they just want to help.
As the trio return from collecting more water, they hear a commotion and discover that Team Rocket is using a bulldozer to ram all the trees, knocking the sleeping Treecko into their net. When they spot Ash, Pikachu, and Treecko, Team Rocket charges at them, sending them flying. After their motto, they take off in their waiting balloon, now covered in neon lights, with all the Treecko in a cage. Ash orders Pikachu to use Thunderbolt, but it turns out that the lights were actually electricity blockers. Ash calls for Taillow, but he quickly realizes that he sent it away to find the others. Team Rocket takes the opportunity to grab Pikachu in a net. But the Treecko that Ash befriended wasn't caught in the net, and now it's angry. It spits its twig at the balloon, but it just bounces off. Team Rocket laughs, and James sends out his Cacnea. Ash doesn't recognize Cacnea, declaring the trio must have stolen it as he checks it out in his Pokédex. Treecko leaps from the top of a tree into the balloon, and starts attacking Team Rocket. Jessie steps backwards and accidentally hits the button that releases the trapped Pokemon. Treecko leaps onto the balloon itself and taunts Cacnea. Cacnea responds angrily with a Pin Missile, but Treecko evades and the attack punctures the balloon instead. The Treecko free Pikachu and they all abandon ship as the balloon flies off into the distance, sending Team Rocket blasting off.
The Treecko that Ash befriended makes up with the old one, but still doesn't want to give up on the tree. Everything seems to be going well until the giant tree suddenly splits in two. The Treecko try to hold it together and Ash gets a rope out of his backpack, but they are stopped when the sun rises, illuminating the tree beautifully. As they look on, Ash and the Treecko have some sort of vision of the tree's life from a seed to the majestic tree it used to be. But the imagining fades and they're only looking at a split, dead tree again, and the two halves suddenly split even more and they fall over completely. A seed rolls from the wreckage and stops at Treecko's feet. Ash takes this as a sign of gratitude from the tree for trying so hard to save it. But Treecko doesn't take kindly to this suggestion and hits Ash. He realizes that Treecko is trying to tell him it's ready to battle.
Ash's friends and Taillow rush onto the scene as the match begins. Pikachu uses Thunderbolt, which Treecko dodges multiple times, before finally scoring a hit. However, Treecko doesn't seem to have taken much damage, and Max reminds them that Electric attacks aren't very effective on Grass-type Pokémon. Ash calls for a Quick Attack, which Treecko dodges. However the evasion manoeuvre leaves Treecko vulnerable, and Pikachu delivers a lot of damage with a Thunderbolt. Treecko hits the ground, knocked out. Max doesn't understand what happened, but Brock explains that usually Electric attacks don't work well because the Grass Pokémon can diffuse the electricity into the ground. Since Treecko was hit in the air, there was nowhere for the electricity to go. Ash throws a Poké Ball and catches Treecko. Ash calls it out of its Poké Ball, and the old Treecko hands it the seed from the dead tree. Treecko promptly plants it, before leaving with Ash and friends as the other Treecko care for the newly sprouted tree.