Richie and Sparky are in the big city, where the nearest Pokémon Center is scheduled for demolition. Two Nurse Joys—a grandmother and granddaughter—are trying to stop the demolition crew, so Richie and his Pokémon step in to drive off the crew's Pokémon. The Nurse Joys tell him that this Pokémon Center opened 75 years ago, back when the area was a rural place where Celebi lived. That was the same day the elder Nurse Joy's friend, Nick, was lost in a landslide. That night, a Celebi appears before Richie and shows him a Celebi carving hidden in the Pokémon Center's furniture. Then Richie is surrounded by light, and the next thing he knows, he's in the middle of a forest!
Richie hears a cry for help, and he rescues a young Joy from falling off a cliff. Joy leads him to the local Celebi shrine, where he's introduced to her friend Nick. Richie is in the past—and it's the day before the Pokémon Center first opened! Nick invites Richie to stay with him and his father for the night. They're traveling carpenters, and they'll leave tomorrow now that their work on the Center is complete. Nick is carving a Celebi statue for Joy but he won't stay for the Center opening and her birthday party, even after Richie tries to convince him to go.
That night, in the middle of a storm, Joy goes missing and everyone in town is looking for her. Nick thinks she's in the forest, so he and Richie go to look for her. They find Joy unconscious, knocked out by a falling tree on her way to check the Celebi shrine. Lightning threatens to set fire to the shrine, and Nick is almost hit by lightning himself as he tries to stop the flames. But Celebi appears to protect him and Joy is so touched, she decides to become a nurse and stay at the Pokémon Center.
The next day, Nick doesn't show up at the party, so Richie takes Joy's Ponyta and rides off to find him. Nick and his father are on a cart headed out of town, but Richie forces them to stop. He tells Nick to be brave and give the Celebi carving to Joy, so Nick and his father turn around just in time to avoid a deadly landslide. As Nick gives Joy his gift and admits his feelings for her—feelings that are mutual—Celebi whisks Richie back to the present. Now, the Pokémon Center is being restored, not demolished, and Nick is the town mayor. The concrete jungle has been replaced with a pleasant, tree-filled town, and Celebi even makes a special appearance before the townspeople.
Ritchie, along with his Pikachu Sparky, arrive in the urban metropolis of Marion Town. While searching for the local Pokémon Center, he comes across an older man polishing a shrine dedicated to the Mythical Pokémon Celebi. Ritchie asks the man where this town's Pokémon Center is, and he explains it's not far and that it is being torn down today.
At the Center, which appears to be an older style, an elderly Nurse Joy and her granddaughter refuse to let the demolition workers pass. While work was to be carried out next week, the workers explain that the Mayor ordered that it had to be tore down today to make way for a new Center. The Nurses still refuse to budge, so the workers send in their Pokémon, a Scyther, Machoke, Rhydon, and Pinsir. However, a Thunderbolt interrupts the proceedings, and Ritchie and Sparky are there, saying they shouldn't be attacking two Nurse Joys. So the workers order their Pokémon to attack him instead. Ritchie retaliates by sending out his Taillow nicknamed Rose, who uses Double Team to trick the enemy Pokémon into colliding with each other. Zippo and Sparky finish the job with a Flamethrower and a Thunderbolt, causing the demolition crew to retreat. The Nurse Joys thank Ritchie, but he brushes it off, saying the Pokémon really deserves the thanks. The Joys invite them inside for some delicious Pokémon food.
Inside, the older Nurse Joy explains that she's about to retire, and she's leaving her granddaughter, the younger Nurse Joy, in charge. They explain that tomorrow is an important day; it's both Grandma Joy's birthday, and the 50/75th anniversary of the Pokémon Center opening. They moan the fact that Marion Town has been growing into a city, and they don't want to leave room for an old Pokémon Center like this one. It wasn't always that way, though. Grandma Joy explains that it used to be a peaceful and quiet town. She even explains that Celebi used to live in the town before it was overtaken by skyscrapers and concrete. This revelation surprises Ritchie. Grandma Joy explains that she saw Celebi the day before the Center opened 75 years ago. A day of joy and tragedy, because the day the Center opened, there was a landslide that took a dear friend, Nick, away from them. She can only sigh, "If only he had come to my birthday party, he might still be alive with us."
That night, Ritchie wishes there was something he could do to help, but he doesn't think there is. Or at least, not until they're surprised by a bright green light which reveals Celebi. Ritchie is amazed, but Celebi flies to a dresser and points at a drawer. Sparky pulls the drawer out, and Celebi flies inside, coming out with a hidden drawer with a Celebi carving inside. Ritchie wonders what it was doing back there, but Celebi answers with another green glow. It time travels Ritchie and Sparky into the past.
Ritchie and Sparky are suddenly confused by their now forested surrounds, but they suddenly hear someone calling for help. They find a young Joy hanging from a cliff, and manage to pull her to safety with some help from her Ponyta. Joy explains that she saw some flowers that she wanted to pick for Celebi when she fell. She explains that legends say that a Celebi lives in this forest, and she shows them an old Celebi Shrine to prove it. A young boy named Nick is working on fixing the doors, but one of them falls off while he's showing off his work. Nick grudgingly admits that when it comes to carpentry, he's still not nailing it. Joy calls him on the bad joke, and this is the first time Ritchie catches his name, and remembers the photo Grandma Joy showed him earlier.
While they're walking back, Joy comments on Ritchie's odd clothes, saying he must come from really far away. She wants to travel when she grows up, though her mother wants her to run the Pokémon Center. When Ritchie asks Nick, he explains that he helps his father. However, Sparky interrupts, pointing out the Pokémon Center ahead, which is still under construction. Joy heads in, hoping to see them at the party. Ritchie looks confused, but Nick explains that it's a two-in-one party: celebrating the opening of the Center, and Joy's birthday. Ritchie suddenly realizes that everything he's seen today is tying in perfectly with what he's heard just earlier.
Nick invites Ritchie to stay over the night at his place. There, Ritchie watches as Nick's father inserts the hidden draw into the chest of draws destined for the Center. With the chest finished, Nick and his father plan to leave tomorrow for another job. Ritchie tries to convince the pair to stay for Joy's birthday party, but Nick's father admits his son is too shy around his crush. Nick adamantly denies it. Later that night during a thunderstorm, Nick's father is informed that Joy ran into the forest. As Ritchie and Nick head out to look for Joy, they find her unconscious near the shrine. As a fire starts near them from a lightning strike, Celebi appears and protects them.
The next day, Ritchie attends Joy's birthday and the Pokémon Center opening. While Nick and his father leave town, Ritchie remembers the Celebi carving that Nick left in the draw and rides a Ponyta after them, hoping to prevent the landslide accident. Upon catching up to them, Ritchie shows Nick the Celebi carving and persuades him to return to give it to Joy. As Nick and his father head back to Marion town, the fatal landslide occurs behind Ritchie. Nick finally shows up to the party and gives Joy her gift – the wooden Celebi carving. Nick also has the courage to confess his feelings, and Joy admits she feels the same. After that happens, Ritchie and Sparky are returned to the present by Celebi.
Upon arrival, Ritchie sees the same demolition crew and their Pokémon at the Pokémon Center. At first, Ritchie believes they are going to demolish it, but they are instead restoring it. Ritchie then meets an elderly Nick who now alive and the mayor of Marion Town. Afterwards, Celebi makes itself known. What used to be an overcrowded and polluted city in one present has developed into a smaller city that still embraces Marion Town's old traditions and nature.