Pikachu, Dedenne, and Wooper have been kidnapped, and after an intense battle with Florges, Goodra is in no shape to go after them! While our heroes start a search, the real motivation behind the attack on Goodra’s home becomes clear: Florges is taking care of a sad little Floette, who needs the spring’s healing water to get better. But now, the water appears to be drying up.
Soon, everyone discovers the truth: the Team Rocket trio are slowly draining the wetlands so they can sell the healing water for profit! Goodra and Florges decide to work together against this common enemy, and their combined efforts soon send Team Rocket blasting off again.
When Ash sees how happy Goodra is to be home, he makes a tough decision and offers to let Goodra stay and protect the wetlands and its friends who live there. After many heartfelt farewells, our heroes are off once again to Laverre City, and Goodra is back home!
Continuing on, Ash chases several Bug-type and Poison-type Pokémon as they kidnap Pikachu, Dedenne, and Wooper. Despite Goodra, Frogadier, and Fletchinder's best efforts, the opposing Pokémon are able to escape. Having reviewed the surveillance data, Clemont and wetlands warden Keanan tell the others that he has discovered Team Rocket's involvement in the recent events. Following Goodra's lead, Ash and his friends leave to find their missing friends. Keanan, meanwhile, decides to stay behind and investigate further.
Meanwhile, at the spring taken over by Florges and her Bug-type and Poison-type army, Team Rocket has put Pikachu, Dedenne, and Wooper into special cages to prevent their escape. Florges worries over her sick daughter Floette, but Floette is not healing because the water is running low and its special healing properties are insufficient to save Floette. Back at Keanan's cabin, Keanan comes to the same conclusion and immediately heads out to discover the cause of the problem. Meanwhile, Ash and his friends arrive at the outer area of the spring, but several Bug-type Pokémon are keeping watch and refuse to believe Bonnie's claims about Team Rocket's treachery since they only listen to Florges, not anyone else. Left with no choice but to battle, Clemont and Serena keep the Pokémon occupied while Ash and Bonnie go with Goodra to find Florges. The three of them enter the spring, but it appears at first glance to be deserted. Suddenly, Florges appears behind them, flanked by two Seviper. Like the other Pokémon, Florges believes Team Rocket's story and refuses to accept Ash and Bonnie's claims to the contrary. Ash and Bonnie then notice the decline in the water level, and as they begin to piece together the story when they realize that Floette is Florges's child, the water begins to drain away completely. At that moment, Jessie, James, and Meowth reveal themselves and their captive Pokémon. They boast about their plan to drain all of the water in the wetlands, and Florges finally realizes that she and her Pokémon army had been tricked all along. Before she can retaliate, however, Team Rocket escapes.
Outside the spring cave, Clemont, Serena, and Keanan watch as Team Rocket's previously hidden airship takes to the skies and prepares to leave, and they meet with Ash and Bonnie again. Ash explains to everyone that Florges took control of the marshlands so she can heal Floette, but the water is now being taken by Team Rocket. Goodra uses its antenna to fling Ash onto Team Rocket's ship, and Florges follows on a Yanmega. Using Dragon Pulse as a propellant, Goodra gives itself enough thrust to board the airship as well. Although Team Rocket tries to shake them off, Goodra blasts a hole in the side of the ship and the three of them enter. They quickly spot Pikachu, Dedenne, and Wooper, and rush to save them, but are confronted by Team Rocket. The conflict quickly escalates into a Double Battle, with Inkay and Pumpkaboo fighting Florges and Goodra. When Inkay and Pumpkaboo target Florges, Goodra steps in and defends her, and when both Pokémon switch their focus to Goodra, Florges stops the attacks and sends Pumpkaboo flying into the control panel for the cages holding Pikachu, Dedenne, and Wooper. Once Pikachu and the others escape their cages, Jessie and James attempt to have Inkay and Pumpkaboo attack again, but they are easily overpowered and sent blasting off by Goodra and Florges.
With the water draining out of the ship, a Yanmega arrives to take Pikachu, Dedenne, and Wooper back down to the surface. Florges loses her balance and falls off the airship, only to be saved by Goodra. However, an untimely explosion sends both Pokémon plummeting towards the ground, and Ash dives after them. Despite the efforts of three Beedrill to save the group, they continue falling until all of the Water-type Pokémon on the ground use Water Gun to save them. With the danger passed, the group turns to other problems - namely, the completely dried-out wetlands. To remedy this, Goodra uses Rain Dance to restore the water, and Florges uses her Grassy Terrain to revitalize the area. At last, Florges is able to revive her Floette, much to everyone's relief.
As the sun comes up the next morning, the Pokémon have all made up with each other and are now living as one large community. As Ash, his friends, Keanan, and Goodra stand on a hill overlooking the wetlands, Ash tells Goodra to stay behind. Now that Goodra has achieved its goal of becoming strong, it can serve as a protector and friend to the Pokémon living in the area. As Goodra and Ash share a tearful goodbye hug, everyone recalls all of the good times they had with Goodra. Ash tries to stop his tears, promising Goodra that no matter what happens or how far apart they are, they'll always be friends just as Dedenne, still crying, jumps up for a hug.
Soon Ash and his friends resume their journey to Laverre City, Ash bidding Goodra, Keanan and the others goodbye as the group leaves the wetlands.