Forty years ago, a young boy named Yukinari hears a voice in the forest.  He remembers being told that if he ever hears the voice of the forest, stay completely still or else he'll find himself in another era.  The "voice of the forest" belongs to the legendary pokemon Celebi, a pokemon who is being chased by a hunter.  As Yukinari goes to assist Celebi, the pokemon decides that the best way to escape is to travel to another time.  The pokemon takes Yukinari with it forty years into the future, to the time of Satoshi-tachi. 

In the present-day, Satoshi-tachi are wandering around the Forest of Ubame when Satoshi spots a Suicune.  Anxious to get a closer look of the legendary pokemon, Satoshi follows it into the forest.  There, he comes across a treetop village where he meets Towa and her grandaughter Miku.  Suddenly, a flash of light is seen coming from the shrine in the forest, so Pikachu runs off to investigate.  At the shrine is Yukinari, the young boy from forty years before.  After he is brought back to the village and is woken up, Yukinari informs the group that Celebi is in trouble.  Satoshi-tachi venture into the forest to find the time travelling pokemon hiding on top of a large tree.  After convincing it that Satoshi and Yukinari are its friends, the two young boys begin befriending the pokemon. 

After a little while of playing, Vicious, an elite member of the Rocket-Dan, appears on the scene and tries to capture Celebi.  Satoshi-tachi manage to ward off Vicious and his giant mecha, hiding deeper into the Forest of Ubame.  Once they're safe, Satoshi and Yukinari play with Celebi and become close friends.  Eventually, Vicious catches up with Satoshi-tachi, but this time he actually succeeds in capturing Celebi with his Dark Ball!  The Dark Ball turns whatever pokemon is captured with it evil, so now Vicious has complete control over Celebi!  Vicious instructs it to start destroying the forest, and the seemingly emotionless pokemon obeys.  Using the debris present in the forest, Celebi creates a sort of vine monster that it uses to attack the forest. 

With a little help from Suicune (who appears after sensing that the forest is in danger), Satoshi is able to reach the summit of the vine monster where Celebi is located.  There, Satoshi reminds Celebi of all the good times they had together and manages to break the spell of the Dark Ball.  Now that Celebi is back to normal, the vine monster falls apart, causing Vicious to retreat.  However, the combination of the Dark Ball's effects and all the energy it used to destroy the forest causes Celebi to become deathly ill!  Satoshi-tachi try to resurrect the pokemon, but it isn't until a group of Celebi transport themselves to the forest (undoubtedly from different eras) to revive the pokemon that Celebi comes back to life.  Vicious makes one more desperate attempt at capturing Celebi, but he is quickly thwarted and left to the villagers for punishment.  With Celebi safe and the forest out of danger, the Celebi transport Yukinari back to his own time.  After Satoshi bids his new friend goodbye, he continues his journey to the next land.