Our heroes are on their way to Laverre City when a passerby recognizes Ash’s Goodra. He introduces himself as Keanan and explains that he’s the caretaker of the nearby wetlands where Goodra used to live when it was a Goomy. Ash and the others are excited to visit Goodra’s old home, but the Pokémon seems reluctant.
When they reach the wetlands, Keanan explains that some time ago, a feud broke out over a healing spring in the area. In the battle, Goomy was launched into the air, where it was carried along by a flock of Swanna until it eventually fell on Ash’s head! The Florges who started the whole thing now controls the wetlands along with its underlings, and Goodra’s old friends have gone into hiding.
With some encouragement from Ash, Goodra confronts Florges in an impressive battle. But just when it looks like Florges has been defeated, an attack from an unknown source knocks Goodra out! Later, the Team Rocket villains (who launched the attack) approach Florges with an offer to join forces. And as Ash keeps watch over a recovering Goodra, the villains grab Pikachu and Dedenne! Will he be able to get them back?
On their way to Laverre City, Ash and his friends stop for lunch. Chespin tries to steal Pancham's food, but the resulting scuffle results in Dedenne's food being spilled. However, Goodra steps in and shares its food with both Chespin and Dedenne, ending the conflict.
As the group prepares to leave, a man named Keanan is driving past, but pulls over when his Bellsprout recognizes Goodra. Keanan approaches the group, and explains that Goodra, when it was a Goomy, lived in the wetlands where he works as a warden. Although Goodra is apprehensive about visiting its homeland, it agrees to go along with everybody else to visit. Curious as to why Goodra left its home in the first place, Keenan reveals the truth. While looking out over the wetlands, Keanan tells them that there is a special healing spring in the area that Goodra used to live near with its friends, but a group of other Pokémon arrived to take the spring by force. During the battle, a Blue Flower Florges ands its army of Bug and Poison Pokémon sent Goomy flying, whereupon it landed on a Swanna's back and was subsequently dropped onto Ash's head. As the group sadly contemplates the story of what had happened, Goodra looks at the quiet wetlands and cries out, recalling the happy memories of its other friends. Keanan reveals that the other Pokémon still call the wetlands home, but they are now confined to a particular corner and hide in secret from Florges and the others.
Elsewhere in the wetlands, Goodra's friend Wooper hears its cry and tries to find Goodra. Wooper quickly follows the sound, and the two Pokémon are delighted to see each other again. Goodra's other friends, who followed Wooper, also come out to greet it. However, several Bug-type Pokémon also heard Goodra's cries and bring it to the attention of Florges, who is in the spring. As Goodra is showing off its Dragon Pulse to its friends, a Swanna comes along and says something to the group, and all of the Pokémon follow Swanna. Although Ash wants to follow Goodra and the others, Keanan stops him, saying that matters between wild Pokémon need to stay between wild Pokémon, but eventually lets him and his friends follow Goodra as long as they stay out of any fights that get started. Goodra's other friends are being attacked by Florges and the other Bug-type Pokémon, but Goodra keeps them at bay with its Bide attack. Rallying behind Goodra, the other Pokémon begin to put up a better fight against Florges's army.
Eventually, Florges comes down to have a battle with Goodra, and immediately recognizes it as the same Goomy she attacked before. Although Goodra is nervous at first, Ash reminds it that it is no longer the weak, frightened Goomy that it once was, and that it will be fine in the battle. After Petal Blizzard and Dragon Pulse cancel each other out, Florges uses Grassy Terrain, thus powering up its Grass-type moves. The powered up Solar Beam from Florges inflicts damage on all of Goodra's friends, putting Goodra on the defensive in order to take a super effective Moonblast for them. Very weak, Goodra almost gives in to Florges, but choice words of encouragement from Ash convinces it to keep going. Goodra's newly learned Ice Beam attack then breaks through a second Moonblast and hits Florges, leaving Goodra as the winner of the battle. As everyone is celebrating Florges's defeat, however, a Shadow Ball and Psybeam attack come out of nowhere and hit Goodra. Simultaneously, a smoke-releasing device shrouds the entire area in a thick black fog that lifts to reveal the disappearance of Florges and the other Pokémon.
That evening, Keanan finishes treating Goodra as Pikachu, Dedenne, and Wooper look after it. Clemont brings up the odd attacks of Shadow Ball and Psybeam, to which Keanan admits no Pokémon in the wetlands can use. Keanan and Clemont then start reviewing surveillance footage. Florges, meanwhile, is resting in the spring as Team Rocket explain their plan to defeat Goodra. It is also revealed that Florges has done all of this to protect her daughter Floette. Listening to Team Rocket's advice, and furthering the evil trio's scheme, Florges orders an Ariados to kidnap Pikachu, Dedenne, and Wooper.