The scene opens
with Celebi desperately hovering through a dense forest away from a Houndoom. The Houndoom
strikes but Celebi dodges. After a few seconds of this a Syther appears. The two pokemon
attack Celebi many times, but its barrier protects it. Finally, Celebi gives in and falls
to the foliage below. A man rides up on a bike and takes out a weird object. He chucks it
at Celebi, who hovers away at the last second. The man orders Houndoom and Syther follow
it.
Sam, a boy about Ashs age, is walking down a path that leads up to a fallen log with a hole through it, making a tunnel. A woman is chasing him from behind. She walks up to him and gives him some food in a dead leaf. He says his goodbyes and walks on through the tunnel. He finds a good place to draw pokemon by a tree. A few Bellossoms are dancing about. They hear something and run away, followed by some other pokemon. Sam looks up to see Celebi being chased by the man and his two pokemon. It just misses his head and continues through the forest. Sam chases after them and discovers Celebi fallen and Syther holding it down with its scythe. Sam tries to help Celebi but the Houndoom attacks him with a flamethrower. Sam ducks out of the way. Celebi cries in pain and a bunch of vines wrap around Houndoom and Syther. Sam picks up Celebi The man rides up and claims Celebi but Sam refuses to give it up and runs. He approaches a shrine that seems to be the one from Ilex forest. Celebi screams again and the forest around them starts to glow a bluish tint. Sam is puzzled when they two are caught in the bluish glow. The glow disappears and Sams sketchbook falls to the grass below.
Vicious, a high in office Team Rocket member, has discovered that the man has been hunting Celebi and comes to his house. The man refuses to tell Vicious anything. Vicious walks out side to a bunch of pokemon in cage; they are the mans pokemon. He smirks when he sees a Tyranitar. He tells his Sneasel to attack the cage. It runs up and slashes the bars in half. The Tyranitar worrily steps out of the cage. Vicious then smirks at the man and pulls out a black pokeball. He throws it at Tyranitar, who is caught in a black glow and gets caught in the ball. Purple sparks exit the ball He releases it. The Tyranitars tint has gotten darker, and it doesnt have the worried look on its face like before. It has become pure evil. Vicious grins and tells it to destroy the area, including the mans residence. The Tyranitar releases a series of hyper beams, and smoke billows around it as the fire destroys the area. Debris falls everywhere and the Tyranitar roars in victory.
The scene shifts to the title and a barrage of leaves are blown by. A drop of water drips off a leaf and hits a puddle of water. The ripples in the water spell out Celebi....
About 40 years later
Misty and Brock are anxiously waiting in the harbor of a town. The boat is ready to leave and the two are worried Ash will not catch it on time. Brock releases Crobat and tells it to go see where Ash is. In a wide alley of the town, Ash is engaged in a battle with a trainer. The trainer sends Croconaw into battle, who releases a few water guns just to show off. Ash chooses Pikachu. Croconaw releases another watergun, which just misses Pikachu. It then goes in for a slash but also misses. Pikachu jumps on Crconaws head, but is shaken off. Pikachu then jumps on a Lantern and uses thunderbolt. A woman and her Pichu watch the battle go on. The two fight a little more, but eventually Croconaw is thrown back into its trainer, and Pikachu thunderbolts them both, ending the match. Ash walks over to help the trainer, but Brocks Crobat flies down and warns Ash hes late. Ash gets to the port but cant get passed a cargo car. The car slowly goes by. Brock and Misty get on the boat. The boat starts to move out of the port and Ash lunges himself at the boat. Brock misses him and Ash falls but is then caught by a white-gloved hand. Ash thanks the person. His name is Towa and he is a guide for the forest on the bank of the river.
Pikachu looks out at the forest and notices a weird blurry pokemon. It is Suicune. Ash sees it too. When Ash tells everyone to look, Suicune runs into the foliage and disappears. They disembark from the boat and Ash calls Professor Oak. Ash tells him how he saw Suicune in the woods, but Oak says thats impossible. Tracey is waving in the background. Ashs Muk smothers P. Oak and Tracey waves good bye and hangs up. Since Ash and co. have a little extra time on their hands, Towa offers to give them a tour of the forest. They take off down the river in a small boat. Team Rocket is spying on our heroes from a hand glider-bike-like thing. Jessie stops her pedaling and James and Meowth cant handle it, and they descend. Ash and co. approaches a waterfall and Towa pulls a lever, which causes the balloons on the boats sides to inflate. They enter the forest and land in a small village like place in the trees. They get out and see the fallen log that Sam went through 40 years ago. They approach it to find an old woman warning them to clear away from there. Her name is Maki. Her teenage daughter Miku approaches. Brock again is in love (obviously). Miku explains to them what happened 40 years ago, but Ash still decides to run through the tunnel.
They walk down the path but stop in their tracks as the forest glows a bluish tint again. Pikachu runs toward the shrine, followed by Ash and Co. When the bluish glow disappears, Sam and Celebi hover there, then fall to the ground. Celebi awakens and hovers behind the shrine. Ash and co approach Sam. They try to awaken him, but he is worn out. Ash carries him (it looks more like a piggyback ride to me) back to the treetop village. They make it to the bottom of the village when Sam wakes up. He instantly thinks Ash has done something rash to Celebi and attacks him. Maki approaches Sam and calms him down. She knows its him but he does not recognize her. She was the woman that gave him the food in the beginning. Maki takes them to her hut and digs around and finds Sams sketchbook. Sam is in disbelief and he looks through it.
A robotic foot smashes down and continues down the forest. Ash and co hear it and Sam decides to go look for Celebi. Ash and co. agree to help. They walk down the road. Team Rocket is stuck in a tree. They look down and see "the twerps" running down the path. Pikachu senses the presence of Celebi and takes off behind the tunnel. Ash approaches a hole surrounded by a bunch of pokemon. He looks inside and sees Celebi. He tries to get it out but, on instinct, Celebi uses its psychic powers to blow Ash, Sam, and some of the pokemon back. Ash runs up and yells at Celebi, who vine whips him and Sam. Sam tells Ash to be nice to it. Ash avoids the vines and says some nice things to Celebi, who comes out and into Ashs arms. They head back to Makis hut. She sees Celebis condition and tells them to go to a pure lake in the forest. Ash and co, and Sam head down a path and see Team Rocket up in the tree. They say their motto when all of the sudden Wobbuffet comes out and the branch breaks, causing them to fall. Ash and the others run away.
The robotic leg seen crashing through the forest belongs to a huge insect-like machine operated by Vicious, who is searching for Celebi. Our heroes bump into him and he discovers that they have Celebi. He claims Celebi but the none of them will hand it over. Vicious gets mad and throws his dark ball, releasing Tyranitar. It attacks them with a bunch of hyper beams. They run away down the path while Team Rocket come and attack Viciouss machine. The 3 realize that Vicious is a superior officer in team rocket and beg for forgiveness. Viciouss Scizor and Sneasel are released. They look at Team Rocket then chase down Ash and the others.
The others continue through the forest when Misty trips and hurts her knee. Scizor and Sneasel appear. Since Misty is hurt, Ash and Sam decide to battle the two pokemon. Sam gets out an old brown pokeball and pushes a switch then opens the ball, releasing a Charmeleon. Ash throws his pokeball and Bayleef comes out, confusing Sam. Scizor battles Bayleef, who uses razor leaf over and over, but is countered by a double team and a hit each time. Sam gives Ash advice to tell Bayleef to focus on its surroundings. Bayleef listens and discovers Scizors position. It uses razor leaf and Scizor falls. Charmeleon simply smashes Sneasel into a rock. Vicious is following the path that Ash and the others ran away on and finds his pokemon each tied to a rock. He smirks and continues on. Team Rocket is also in his machine.
As Ash and co continue on, the forest gets foggy. Celebi is getting worse. The approach an Ursaring and a Teddiursa. Sam looks at the two pokemon and relays to the others to follow them. The two pokemon lead them to a Stantler. The Stantler takes off towards a Furret. The Furret leads them to the pure lake. Sam brings Celebi into the lake. It goes towards the middle and sinks under the water. It soaks up sunlight and the water and it begins to glow. Many pokemon have gathered to see the sight. Celebi flies out of the water and approaches them. Celebi blissfully flies around them and Ash and Sam follow it into the water. They swim with a bunch of water pokemon when they suddenly run out of air. Celebi helps them to the surface with its psychic powers. It then uses its powers to make them fly. The fly happily through the sky. Celebi flies down to Misty and touches her knee, which instantly heals. She thanks Celebi. Celebi continues through the forest, followed by the others.
Celebi finds a tree full of berries and takes one and gulps it down. It loves them and starts doing a little jig while eating. The others look up and also take one. They love them too. Ash takes some more for later. They walk a little more through the forest then make camp. During the night, Ash awakens to find Sam drawing in his sketchbook. Ash sees that his is drawing Celebi and Pikachu while they rest on each others shoulders. Sam shows Ash a few of his sketches and they talk a bit, but Sam seems troubled. He gets up and walks away. Ash gets up and goes after him. Ashs stomach starts to growl and he does his little hehe laugh to show hes embarrassed. Sam pulls out the food he was given to by his mom and breaks it in half, giving Ash one of the halves. Pikachu hears Ash and Sam talking and wakes up. Pikachu goes towards them and Celebis head falls from Pikachus shoulder to the ground. It wakes up and follows Pikachu. They all see some Metapod and run towards them. They are all evolving into Butterfree. Ash, Sam, Pikachu, and Celebi watch the Butterfree as they fly past the sun, which is just appearing over the horizon. They climb a tree to get a better look at the Butterfree as they sprinkle their powder. Ash and Sam put their arms around each others shoulder, which kind of seems sort of strange to me.
The sun rises and Ash and co prepare to head back. They continue down the path past the shrine when Vicious steps in the way. He demands Celebi again and uses a claw-like thing to try and get it. Jessie and James walk up behind them with Butterfly nets, and Ash and co decide to fight. (come on, butterfly nets, ash and co got past a lot worse then that from team rocket) The claw goes in for Celebi but it dodges out of the way. Pikachu uses thunderbolt on the machine, but it hurts only Team Rocket. The claw tries again and this time it grabs Celebi. The claw then shocks Celebi, weakening it badly. Vicious then pulls out his dark ball and throws it at Celebi. Unable to fight back, the dark energy surrounds Celebi and it is captured. The purple sparks emit from the ball again and Vicious looks quite pleased.
Ash looks up at Vicious and gets angry. He walks up to the leg and starts to climb it. A group of Pidgeys "help" him up there. Ash wrestles with Vicious for a while and grabs Celebis darkball, but Vicious throws him down. Vicious walks down and puts his foot on Ashs hand. Ash tries to hold out, but the ball is taken from him. Vicious then throws the ball to release his new evil Celebi. He tells it to destroy everyone and it uses its psychic powers to push everyone away. Celebi then starts making massive wind appear. Tree parts swirl in the wind and form together as Vicious laughs. Jessie gets pulled in as well. At Makis house, Maki, Miku, and Towa look up at the ball of branches and stuff and get in Towas balloon to go after it. The scene shifts to a small valley at the foot of a mountain. Suicune rushes along the mountain. It feels that something is not right and takes down to the valley below.
Pokemon are trying to outrun the swirling fortress of tree parts with massive spikes. Vicious orders Celebi to bring it to the lake. Jessie is tangled in the mass and tells Vicious she wants out, but he just laughs. Celebi then starts to change the mass into a ghoul-like monster. Celebi is in the middle of the head, controlling the beast. Maki, Miku, and Towa approach Ash and co and give them a ride toward the monster. Vicious looks up and sees the balloon that they are in. He orders Celebi to destroy it. The monster shoots a purple beam, which hits the balloon. The balloon smashes into the pure lake. Celebi sends another beam, which hits the pure lake, which then goes impure. The monster then keeps heading towards the lake. Meowth and James are in the lake hanging on to a branch, depressing isnt it? Ash and Sam rush towards the monster. Pikachu tries to shock Vicious, who jumps out of the way to a tree branch nearby. Celebi sends a beam straight towards them, with hits the ground with a massive impact. All of the sudden, Suicune exits the smoke with Ash and Sam atop its back. Vicious knows that Suicune is also rare and jumps down from the tree branch. He sends out Tyranitar. Brock sends out Onix to battle the Tyranitar. Onix tries to tackle it, but Tyranitar grabs its head as it hits. Onix gets beaten easily. Suicune has to save it by firing a bubble beam at Tyranitar, taking it out. Onix tries to pretend it won and tosses it into the lake, glory hog! Brock then recalls Onix.
Suicune tries to bubble beam Celebi, with no luck. Celebi just gets angry and grabs Suicune with its vines. It gets shocked by purple electrical charges, like the ones that emit from the dark ball, only more powerful and bigger. Vicious smiles in victory. Sam and Ash jump off Suicune in order to save Celebi, and probably so they dont get shocked too. They enter the monster and yell for Celebi to cease. Celebi hears them and remembers the time they swam and flew together. It grabs its head and stops. Vicious looks up to see Suicune being unharmed and yells for Celebi to keep attacking. It begins again, and hears Ash and Sam yell for it to cease again, and this time remembers when they all ate at the berry tree. It grabs its head again and screams, but begins attacking again. Ash and Sam climb to the head and tell it to cease once more. Celebi remembers the time when they all watched the Butterfree fly across the sky and stops all together. Jessie screams from inside the monster. Pokemon and human watch as the monster starts to decay. Celebi uses its psychic powers to float Ash and Sam down to the lake. Suicune gets out of the vines. Vicious wonders whats going on and then gets smashed off the remaining pieces of the monster when Celebis dark ball explodes. Jessie falls into the lake with the rest of the branches. James and Meowth watch from behind a tree. Celebi looks like it is decaying. Sam says to bring Celebi into the lake again, but the water isnt pure anymore. Sam remembers that Suicune can purify water with each step. Ash tells Suicune to and it walks into the water. It starts to glow and jumps around the lake, leaving pure water behind where it landed. The water is totally clean and Ash places Celebi in it, but the water still has no effect. Ash takes out a berry and tries to make Celebi eat it but it doesnt move. Everyones faces turn sad as the now think that Celebi is dead. Ash and Sam start to cry, and the others start to too. The pokemon that have gathered all cry out, even Suicune. All of the sudden, a bright light appears on the lake. Everyone looks up to see many Celebi dancing around in the light. The original Celebi starts to glow and floats up. The other Celebis dance around it and the forest glows gold. Celebi is revived! Celebi looks down at Ash and the others and the other Celebis fly up toward the sky and disappear. Celebi watches them go and then flies down to the group. It flies by the water when Vicious jumps out and grabs Celebi in his hands. He attempts to escape by firing off a jetpack. Ash and Pikachu jump after him and catch his leg. Vicious moves his leg back and forth, but Ash wont let go. Pikachu shocks all of them, causing the jetpack to explode. Ash grabs Pikachu and waits for his certain doom when Celebi uses its psychic to bring Ash safely to the others. Vicious, however, falls down through the trees and lands at Maki, Miku, and Towas feet. Viciouss armor saved him, but it wont save him now. His helmet has fallen off and he can see the many pokemon that are angry. Towa makes a fist to prepare for the fight. Vicious reaches for his pokeballs, but discovers that he left them tied to the rocks. The pokemon tie him up and leave him there. Celebi floats down to Sam and opens the time portal to take him back. Everyone says goodbye to them and Ash starts to cry as his new friend leaves. He waves desperately as Sam goes through the portal.
Sam appears at the shrine. He looks around for Celebi, but it is gone. Maki runs up to him and what happened. He says hes fine. Jessie floats in the lake. Meowth and James approach her in a small boat. They yell at each other for a bit when the Tyranitar splashes out of the water and destroys the boat. It swims to the shore. They 3 seem happy just to float in the lake for a while. Scizor and Sneasel look around for Vicious, then realize they are free.
During the credits
Towa takes Ash and co away from the village and past the waterfall toward the city they started the tour from. Back at Professor Oaks lab. Tracey accidentally makes a bunch of books fall. He discovers Sams sketchbook and flips through it. He finds the picture of Pikachu and Celebi, and wonders if he should ask Oak about it. He decides to wait for the right time. Ash and co look out at the sunset from a dock. Suicune runs back into the forest. Ash and co travel a little bit more and come across a tree with berries like the one before. Something is spying on them as they eat at the shoreline.