Ash Ketchum arrives with Misty and Brock in Johto's Arborville. Near a riverbank, they spot the legendary Suicune. Ash contacts Professor Oak, who confirms a past encounter with Suicune before the call disconnects. Local Mr. White guides them into a forest where they meet Towa and her granddaughter Diana. Towa warns of the "Voice of the Forest," revealed to be Celebi. A boy named Sammy and the injured Celebi then emerge from a time portal. While Celebi hides, Sammy struggles with having traveled 40 years into the future. Ash, Sammy, Misty, and Brock find the wounded Celebi and decide to take it to the healing Lake of Life.

Guided by wild Pokémon, they reach the lake where Celebi recovers. Ash bonds with Sammy, hoping he can return to his own time. The next day, the rogue Team Rocket operative Iron Masked Marauder attacks. Using a Dark Ball, he captures Celebi, corrupting its powers to encase it in draconian armor formed from the forest. Revealing his plan to overthrow Giovanni and dominate the world, the Marauder battles Ash, his friends, and Suicune.

Ash, Sammy, and Pikachu penetrate Celebi's armor, urging it to resist. Celebi breaks free from the Dark Ball's corruption but collapses and dies upon reaching the lakeshore. Suicune attempts to purify the lake to revive Celebi but fails. Multiple Celebi from across time then appear and collectively resurrect their kin. The Marauder tries to abduct the revived Celebi, but Ash and Pikachu intervene, rescuing it while the Marauder crashes nearby.

Celebi returns Sammy to his original time; Sammy promises Ash they will meet again. Later, recounting the adventure to Professor Oak, Ash grows sad about Sammy's departure. Oak reassures him that friendships endure across time. After ending the call, Ash and his companions realize they never mentioned Sammy's name to Oak. In his laboratory, Oak reviews a sketchbook, revealing he is the adult Sammy. Tracey later stores the sketchbook, preserving this secret.