Near Mr. Coronet, Ash and his friends come across Pokémon Hunter J's goons trying to snag a group of wild Shieldon. Ash is about to come to their rescue, but his old friend and rival Gary gets there first with his Electivire. Once the men are gone, Gary explains that he's here in Sinnoh as part of a project to turn the area into a nature preserve for the Shieldon. Now that J's men are looking to kidnap them, Gary decides to move all the Shieldon to a safer location, and our heroes decide to help.
Pokémon Hunter J's minions aren't about to leave a valuable prize alone, and it's not long before they show up again to capture the Shieldon. Ash is ready to give J's men the battle of their lives, but Gary doesn't want to risk getting into a fight that could injure the Shieldon. Instead, Gary stirs up a Beedrill nest, and the angry Beedrill keep the minions distracted so our heroes can make a getaway.
As Gary and Ash lead the Shieldon on a perilous escape route across nearby cliffs, Pokémon Hunter J figures out where they're headed and shows up on her Salamence to steal the Shieldon herself. Despite Gary and Ash's best efforts to hold her off so Dawn and Brock can get the Pokémon to safety, J still manages to snag one Shieldon and escape. Determined to put a stop to her crimes, Gary and Ash sneak back to her base and bust their way through in order to get Shieldon back. J is about to take them on when she gets word that her original client no longer wants to purchase the Shieldon; with no money on the line, she's no longer interested in the Shieldon and immediately leaves. The Shieldon are safe again, but who knows where J will strike next?
At Mount Coronet, Ash, Dawn, and Brock encounter a Shieldon. Just then, a vehicle containing J's henchmen appears. Ash tells his Pikachu to use Thunderbolt. The henchman responds by sending Golbat which avoids Pikachu's attack and hits him with Wing Attack.
Suddenly, Gary appears with his Electivire, who hits J's henchmen with an Electric-type attack. Electivire picks up Shieldon and runs away along with Gary and the group. As they are running, Brock explains to Dawn that Gary was a rival of Ash’s. They soon arrive at a hidden area, where they are greeted by other wild Shieldon. Gary explains that he is part of a project that aims to make a part of Mt. Coronet a Pokémon preserve. He gets his laptop out of his backpack and contacts Professor Rowan, telling him about the Pokémon hunters. The Professor orders Gary to escort the Shieldon to a specified location, depicted on a digital map, where they will meet up. Ash offers to help and Gary agrees, thanking him.
Meanwhile, Team Rocket plots their revenge on J by stealing her collection of Pokémon. Suddenly, the same vehicle appears, and Electivire picks the Shieldon up and rushes off with them into the forest. Gary sends out his Blastoise, which uses Water Gun on the vehicle. Pikachu uses Thunderbolt and stops the vehicle. The same henchman from earlier emerges and sends out Golbat, which knocks out Blastoise. Gary sends out Umbreon which uses Sand Attack on Golbat. It responds by using Air Cutter, but Umbreon dodges the attack which instead hits a tree, causing a swarm of angry Beedrill to come out. Gary recalls Umbreon and Blastoise, and the Beedrill head for the henchmen while the group escapes.
Later, J talks with a client about the Shieldon and she gives instructions to move on out and surround the area. Ash and the group are forced to hide among the shrubs from the henchmen. Ash suggests they attack, but Gary calls this idea reckless and suggests they focus on protecting the Shieldon. Gary takes his laptop out to plan a new route. They traverse a steep mountain trail by walking along the rock face. One of the Shieldon panics and almost falls down dragging the others with it before Ash quickly grabs them by their rope. With the help of the others, they manage to pull the Shieldon back up.
Meanwhile, Team Rocket is sneaking into J's base when a surveillance camera spots them. They start to recite their motto, but the henchman interrupts when he activates some trap walls. J, meanwhile, flies down on her Salamence and greets her goons on the ground. From the base, one of her henchmen alerts J through her headset that a vehicle, carrying Professor Rowan and his lab assistants, has been spotted near Mt. Coronet. J deduces that it must be an arranged meeting, and promptly flies over to the vicinity. Having just received an update from Rowan that he and Officer Jenny are close by, Gary is taken by surprise to see Hunter J. She attempts to use her capture device but Pikachu stops her with Iron Tail. She responds by sending out Drapion which uses Cross Poison on Pikachu. Gary sends out Blastoise again which uses Hydro Cannon, but Salamence counters with Hyper Beam. As Dawn and Brock are escaping with the Shieldon, one of the Pokémon slips and falls, leaving it exposed to J, who uses her capture device on it. After witnessing this, Ash orders Pikachu to use Thunderbolt but Drapion blocks it. J orders Drapion to use Pin Missile and Salamence to use Hyper Beam. Ash responds by ordering Pikachu to use Thunderbolt while Gary has Blastoise use Hydro Pump, but J's Pokémon's attacks overwhelm theirs.
Next, Brock, Dawn, and the Shieldon meet up with Professor Rowan, his assistants, and Officer Jenny. They inform the Professor that one of the Shieldon was captured by J. Meanwhile, J takes possession of the captured Shieldon and enters the vehicle while Ash and Gary hold onto the undercarriage. The vehicle arrives at the base, and Ash sends out Staravia which flies away, unseen by J, to find the others. The vehicle enters the base while J's client in a helicopter is seen preparing to land. Inside the base, Ash and Gary use their Pokémon to sabotage the base freeing Team Rocket in the process. An explosion occurs and Ash jumps out of the smoke grabbing Shieldon and unfreezing it. As J prepares to call out one of her Pokémon, the client informs her the deal is off to avoid being arrested, as Officer Jenny is nearby. J and her henchmen also withdraw. Rowan, Jenny, Brock, and Dawn arrive. Officer Jenny is glad the Shieldon are now safe and adds that she will launch a full investigation into Hunter J. Gary thanks Ash for his help, telling him that they'll be friends to the end. Later, the group says goodbye to Gary, Jenny, and Rowan as they depart on their road.