The story begins in a strange and luxurious forest. A legendary Pokemon called Celebi is pursued by a fierce Houndoom. Its psychic barriers enable it to resist against the attacks of demonic dog until the arrival of a Scyther to help the enraged Houndoom.
Celebi does not stand long against both Pokemon and falls in the grass.
Then comes a man, some sort of hunter that Houndoom and Scyther blindly obey (as if they couldn’t see evil in that man). He is about to capture Celebi, but fortunately, it manages to break free and escape.
Meanwhile, a young boy named Sammy makes a painting of a Bellossom. But his inspiration is troubled when he overhears Celebi pursued by Scyther and Houndoom.
The young man, wondering what’s going on, abandons his painting to follow the strange pursuit.
A few miles away, he finds Celebi in very bad shape and runs to help it and fled afterwards.
The Hunter reappears and asks Sammy to give him Celebi. However, Sammy ignores it and continues to run away. Sammy managed to find a strange altar, which suddenly begins to flicker.
Celebi cries and the forest becomes engulfed by a strange light, bluish light which engulfs Sammy and Celebi.
50 years later, we find Brock and Misty in a port city. They have been waiting Ash since 2 hours. He is actually doing a Pokemon Battle on the town square. Pikachu fights against Croconaw and wins the match, but our young hero suddenly remembers Misty and Brock, they are waiting to go on a boat.
Ash leaves the town square and runs to the port. Misty and Brock sees him, and then to enter the boat and says that Ash will join them, but when he reached the dock, the boat has just left! Ash is jumping from platform to platform to go on the ship. He just missed his shot, but luckily he is saved by an old man.
Ash thanked his savior, an old man called Mr. White, a kind tour guide who works in a forest nearby.
Meanwhile, 50 years in the past, we learn more about The Hunter. This man is a prominent member of Team Rocket, but not much is known about him, exept that he steals other people’s Pokemon with Dark Balls that turns them into Dark Pokemon. He then notices a Tyranitar. A smile animates the face of The Hunter, as if he was sadistic. then he threw a Dark Ball on Tyranitar.
The darkness flowing from those balls completely changed Tyranitar. The Hunter ordered it to destroy his former master, and the Tyranitar obeyed without hesitating.
During the boat trip, Ash see Suicune, but it dissapears.
Once there, the tour guide offers Ash to come for a walk in the forest where he works. Ash agrees. In the forest, Ash meets a wonderful girl that Brock, as usual, cannot resist.
At that time, the forest begins to ripple and becomes all blue. Some kind of glow in the distance draws Ash. As he approached, he finds Sammy and Celebi coming out of the light. But Celebi went back to the light and vanished.
The forest returns to normal, and Ash decided to bring back Sammy the village.
During the journey, the young man comes to awakens, but doesn’t know where he is and wonders where’s Celebi.
A few days later, Ash and Sammy got to know each other and took a walk in the forest. They arrived near a tunnel. Sammy remembers going there during his getaway with Celebi.
In searching around, Ash arrives near a hole where hundreds of Pokemon have joined. They try to cure Celebi who was seriously injured after a pursuit that happened 50 years ago.
Ash approaches. Celebi is not as cowardly as its friends, which are fleeing in every direction.