While our heroes are stopped at a Pokémon Center, Squirtle runs off—never a good idea when Team Rocket is lurking nearby! May finds Squirtle at an empty train station with an old lady, Edna. Edna's granddaughter Katrina tells May (and an eavesdropping Meowth) the story: Grandpa Jonathan left to become a Pokémon doctor, but Grandma Edna didn't want to leave town. She changed her mind when she realized they were going to have a baby, but she missed his train and he passed away in an accident before she could see him again.
After May returns to the Pokémon Center, Squirtle disappears again. She goes to the train station and finds Meowth pondering Edna's story. Then she sees Squirtle, who's found Edna's old locket. A bright light envelops all three and they're transported back in time! May spots Jonathan and realizes this is the day he leaves for the city, but she can't enter the train station without a ticket.
Thinking fast, May and Meowth use a hot air balloon and Squirtle's Ice Beam to turn rain clouds into snow. Jonathan's train is delayed and Edna catches up in time to tell him about the baby. Then our trio returns to the present day just in time to see May's Pokémon Egg hatch into an Eevee, watched over by Jonathan and Edna. Not only have their lives been changed, but the entire town is better than ever! May and Meowth look on, happy to have done a good deed.
Nurse Joy greets Ash and his friends at the Pokémon Center in Fuchsia City, immediately noticing May’s Egg. Brock stops feeding his newly obtained Bonsly to try and woo Joy over. However, Bonsly attacks Brock knocking him to the ground. Bonsly cries as Munchlax slurps down its bottled formula for itself. Brock picks Bonsly up to comfort it and lessens its pain. Nurse Joy advises Brock that there is plenty of food in the cafeteria, so Brock carries Bonsly over to feed and Max escorts Munchlax as well. Ash decides to continue training for his Battle Pike match, and Squirtle also follows him outside. May is alarmed and heads after Squirtle.
Meanwhile, Team Rocket spies on the twerps from their treetop location, plotting to capture Pikachu. James spots the stray Squirtle running off into the distance as May trails behind. At Jessie’s suggestion, the trio splits up to better their chances of stealing a Pokémon. Squirtle finally stops running as it comes upon an abandoned train station, and May follows it inside. May steps out on to the platform where she finds Squirtle in the arms of an elderly woman, Edna.
A soft rain begins to fall as Edna explains that she is waiting for someone to arrive on the next steam train service. May is perplexed as the station is clearly abandoned, though Edna is determined to wait. Edna’s explanation is cut short as her granddaughter Katrina rushes in, frantically looking for her. Edna becomes sombre as Katrina tells her it is time to go. Edna grabs her umbrella and proceeds to leave the platform, disappointed that she once again missed the train service. The rain reminds her of the day that he went missing, and she wishes it had snowed that day. May notices a picture lying on the bench where Edna is sitting, which resembles Edna in her younger days. Seeing the photograph, Katrina details Edna’s tragic past to May while Meowth spies on them. Edna used to own and operate a Pokémon breeding Center where she cared for and nurtured Pokémon Eggs alongside her husband Jonathan. Jonathan left the Fuchsia for the city to study medicine, though Edna refused to leave her hometown. Having read Jonathan’s goodbye letter, Edna ran to the station to stop her husband leaving and inform him that she was having their baby. Though she narrowly missed the train service that day and lost her locket after bumping into a stranger on the platform. A year later, Edna received news that Jonathan had passed away in an accident, leaving her heartbroken. Katrina explains that her grandmother refused to believe the letter and has attended the train station everyday awaiting Jonathan's return.
In another location, Ash begins his training as the ever devious Jessie is just feet away spying on his actions. Ash continues his Volt Tackle training with Pikachu as an electrical force begins to rotate around Pikachu's body as it blasts through a boulder. The rubble hurls towards Jessie's location and collides into her. Pikachu lands as the force dissipates and Ash commends Pikachu for his agile movements. Meanwhile, James spies on Brock and Max inside the Pokémon Center as they devour the food inside.
Nighttime falls and May's Egg begins to glow a faint white. Nurse Joy kindly offers to take Egg from her and explains that it is about to hatch soon. Max notices that Squirtle has disappeared again, so May immediately rushes to the abandoned train station to find it. Instead she finds Meowth sitting on a platform bench. Meowth explains that he is taking some time to think about Edna’s tragic story. May is unimpressed to learn that Meowth was eavesdropping, but he tells her to get off his back. Suddenly a familiar sound alerts May to Squirtle as it stands on the tracks pointing to something - Edna's lost locket. As May opens the locket she notices a picture of Edna's husband. A mysterious light begins to emit from the trinket as it then envelops May, Squirtle, and Meowth, transporting them back in time to when Edna's husband is about to make his departure.
A train roars down the track, forcing the trio to dash for the train platform. A station attendant scolds them for playing on the tracks, so the trio flee from the station to avoid further trouble. With the now bustling town in front of them, they quickly come to realize that they've been transported back in time to the exact moment when Edna's husband begins his departure. As they begin to try to explain the situation to each other, Edna's husband walks passed and enters the station. May sprints into action, hoping to change Edna’s future for the better. However, the same attendant from before stops them walking onto the platform and removes them for the station. As Edna reads the letter left by her husband and heads for the station, May and Meowth hop inside a hot air balloon and ascend into the air. The last calls for the train are heard as Squirtle begins to aims its Ice Beam at the sky. As hoped, a faint snow begins to fall, causing the train to delay its departure. Edna successfully reaches the station and this time manages to find Jonathan to inform him that she is pregnant. Edna and her husband walk outside to notice the solitary fir tree covered in snow and glistening with color, created by Volbeat and Illumise in a courtship dance. The town has dubbed this phenomenon as the "Lights of Joy".
The mysterious light emits from the amulet once more as May and Meowth are then returned to their own time. The trio are again forced to flee the tracks to safety as a train approaches. As they walk outside, Fuchsia City is now flourishing with citizens as Ash and friends rush over to May's location and alert her that her Egg is about to hatch. They rush to the Pokémon Center where they are greeted by Pokémon pediatricians Edna and her husband Jonathan, who are helping the Egg hatch. May is startled by the array of changes resulting from her trip to the past, as neither Edna, now with her locket around her neck, or Katrina recognize her. As the Egg grows ever so brightly, the light begins to dissipate to reveal an Eevee. Jonathan remarks that Eevee is healthy before handing it to May. Outside the Center, Jessie and James confront Meowth as they prepare to capture Pikachu. Meowth, having traveled back in time to rewrite Edna's tragic past and watched Eevee hatch, declares that he has no interest at the moment and promptly walks off. His teammates are left baffled. As night befalls, the fir tree glistens with the "Lights of Joy". With her newly forged friendship between Eevee and herself, and seeing Edna happy with Jonathan, May looks forward to the adventures and battles that await her.