Ash finds Sam alone in the forest as Celebi has fled. Sam awakens and discovers he is 40 years in the future from when he was. He, Ash, and the others search for Celebi and they find it in a tree. After some convincing, the gang manage to gain Celebi's trust. They run into a high-ranking member of Team Rocket, the Iron Masked Marauder, who has been trying to capture Celebi. Jessie, James, and Meowth also team up with the Iron Masked Marauder to capture Celebi.
The heroes take Celebi to its home, the Lake of Life, where it is healed by the water. The group spend the night in the forest. The next day, Celebi is captured by the Iron Masked Marauder and is turned evil by the Dark Ball, a ball with special powers that will enhance the captured Pokémon's powers and turn it evil. The Iron Masked Marauder orders Celebi create a giant dragon made from parts of the forest. The heroes chase after Celebi in Maki's flying boat, but are brought down by the evil Celebi's attacks. The Iron Masked Marauder tries to kill Ash and Sam, but Suicune saves them. Onix and Suicune do battle with the Masked Marauder's evil Tyranitar, while Ash, Sam, and Pikachu clamber into the dragon and manage to get Celebi to remember its memories, successfully bringing Celebi back to normal.
With the destruction of the dragon shape, the Iron Masked Marauder falls into the lake. The other heroes rush to the lake's edge and find Ash and Sam with Celebi, who suddenly falls limp. Ash and Sam realize Celebi is dead and everyone weeps. However, the Voice of the Forest materializes in the sky and thousands of Celebi appear and resurrect Celebi. The Iron Masked Marauder appears and kidnaps Celebi and flies up with a jetpack, but Ash and Pikachu hold onto him as he flies away. Pikachu destroys the Masked Marauder's jetpack and they fall to Earth, but Celebi saves them. The Iron Masked Marauder falls down to the forest floor and is confronted by the old woman, her granddaughter Diana, Maki, and the Pokémon of the forest.
Celebi prepares to bring Sam back in time. He has an emotional farewell with Ash and departs with Celebi. Before Ash leaves the town into his next journey, he talks to Professor Oak about what happened, and muses about the story. Professor Oak tells a sad Ash that he and Sam are going to be friends forever.
After Ash, Brock, and Misty get on the boat, Professor Oak had Sam's notebook saying "Hmm... it seems like it only happened yesterday". The ending credits shows Tracey cleaning Professor Oak's room and finding Sam's drawing pad, containing the faded sketch of Pikachu and Celebi. (The reason Professor Oak had the notebook was because Sam was the young version of Oak, whose first name is Samuel.)
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