The episode starts with Ash and Pikachu having just finished shopping. Rotom offers to carry a shopping bag but ends up dropping it, causing a doughnut to fall out. Anela from the marketplace picks up the doughnut and returns it to Ash, but the doughnut is immediately intercepted by Litten. The group chases after Litten and finds it under a bridge giving the doughnut to Stoutland. Ash realizes that this was where Litten and Stoutland moved after their first encounter and observes how Stoutland is teaching Litten how to use Fire Fang. Although Litten accumulates enough strength to pull off the move, it fails to maintain the intensity at the last second. Ash's group goes down to visit Litten and Stoutland. Litten initially turns down Ash's offer of food until rebuked by Stoutland. As Stoutland continues to mentor Litten, Ash observes Stoutland deteriorating health.
That night, Professor Kukui reviews video footage Rotom took of Litten and Stoutland, remarking that it's rare for two completely different species of Pokémon to work on moves together in such a close way.
The next day after school, Ash suggests to Pikachu that they should go visit Litten and Stoutland again. Upon saying this, Team Rocket appears out of nowhere, but their motto gets interrupted when Litten suddenly attacks them with Ember and comes running up to Ash, asking him to follow. Ash commands Pikachu to use Electro Ball on the ground, using the distraction to disappear with Litten. While Jessie and James decide to retreat, Meowth insists on going after Litten and runs off to find them.
Upon arriving under the bridge, Ash sees Stoutland has collapsed on the ground. Rotom declares that Stoutland is undergoing severe breathing problems, and Ash decides to carry Stoutland to the Pokémon Center on his back despite Stoutland's size. Nearby, Meowth watches on silently, as a nearby withering tree sheds more of its leaves.
At the Pokémon Center's emergency room, Ash, Pikachu and Litten watch as Nurse Joy and her Pokémon take care of Stoutland. As soon as the door opens, Litten rushes inside the ward as Nurse Joy and Ash discuss Stoutland's condition. Outside, Ash asks Nurse Joy if Litten knows the truth behind Stoutland's condition, and Nurse Joy replies that she can sense it does. Ash then calls Professor Kukui and gains permission to stay the night. Later that night, Ash brings food for Litten and Stoutland, only to find them missing from the emergency room. Knowing where they have gone, Ash and Pikachu run out to look for the two Pokémon, coming across Meowth. Much to Ash's surprise, Meowth tells them that he wants Litten to be protected. Stoutland, back under the bridge, attempts to teach Litten once more how to use Fire Fang, but Litten fails once again. Stoutland then falls asleep and Litten curls up next to it.
In a dream, Litten stands in a white void and sees Stoutland in front of it, prompting it to run up to Stoutland but unable to catch up as Stoutland drifts away into the distance. Waking up, Litten finds that Stoutland has gone missing, and begins searching for Stoutland at their old hideout, the market and a cliffside, but is unable to find Stoutland. Upon returning to the bridge, Litten witnesses the couch Stoutland had been resting on finally break as the final leaf falls off the dying tree. Looking up at the bare tree, Litten realizes that Stoutland is gone forever and begins to howl as rain begins to fall. Carrying umbrellas, Ash and Professor Kukui come to visit Litten. Professor Kukui, realizing that Stoutland has disappeared, bows his head and apologizes. Litten curls up on the broken couch, falling asleep. Back in Team Rocket's hideout, Meowth looks sadly up at the sky. Bewear offers him a gentle hug, drawing a stiff response from Meowth that he isn't in the mood. Following this, Ash receives some food from Anela, who tells him that Litten is welcome to visit any time. Returning to the bridge, Ash offers Litten the food, but Litten refuses to eat.
Ash spends the day staring out in the rain concerned about Litten. Back at the bridge, Meowth is seen asking Litten to tell him what happened, but quickly runs off as he sees Ash approaching. Ash tells Litten that he and his Pokémon will stay by its side until it starts eating again.
By the time the rain stops, Ash and his Pokémon have fallen asleep with Litten. Rousing awake, Litten sees a rainbow and a cloud formation that resembles Stoutland. The sight convinces Litten to accept what happened to Stoutland and move on. Waking up as well, Ash offers a Sitrus Berry but Litten pushes it back to him. Ash then asks Litten to become his Pokémon, saying that he wants to help Litten master Fire Fang. Litten initially seems to agree, but attacks Ash with Ember. Nearby, Meowth muses that Litten wants to battle Ash for it, having decided that it doesn't want Ash's pity.
Ash uses Pikachu, trading many attacks with Litten with neither side having a distinct advantage. Eventually, having fought to a standstill, Ash asks Litten if it accepts him as his Trainer, and Litten agrees, jumping into a Poké Ball Ash throws in the air. Meowth leaves, knowing that Litten's capture is ultimately for the best, and remarks that he and Litten are enemies from now on. Ash then sends out Litten who is greeted by the other Pokémon, and they share the food Ash had brought along.