Upon working to help regrow the forest, Quagsire's abilities leave everyone amazed — and that's not the last Pokémon surprise!

Liko and Roy arrive to find a forest in ruins. The gang aids an injured Wooper and seems to anger the Arboliva — could there be something bigger at play?

In the town of Artazon, Liko, Roy and top trainer Nemona meet up with the artist Brassius, who recounts his dark encounter with the black Rayquaza.

The crew enjoys Paldea, but Liko's joyride hits a bump. First she faces a charging Lechonk — then she must decide if it's time to abandon ship.

Food is mysteriously running low, prompting the crew to stop and shop. Meanwhile, Liko aims to get near Dot... never imagining just how close they'll be.

Liko and Roy ask about Rayquaza's whereabouts from Dot, the crew's reclusive information gatherer, but she rebuffs them with a drawing of a defeated Roy and Hogator. Friede obliges to train Liko and Roy in Pokémon battling, pitting them against his partner, Captain "Cap" Pikachu. When their usual strategy of blindly ordering attacks fails, the two improve by focusing on Cap's movements, although Nyahoja and Hogator lose interest in the match and fall asleep. Liko and Roy apply their newly gained knowledge in battle against other, which ends with Nyahoja learning Quick Attack and defeating Hogator. Dot responds to their match with a drawing of Rayquaza flying over Paldea, indicating the legendary Pokémon to be there.

After Liko is protected by her pendant, she and Roy battle Amethio together, but his Soublades easily overpowers Nyahoja and Hogator. As Liko rushes to protect Nyahoja, Roy's Poké Ball resonates with her pendant and unleashes a black Rayquaza that sends the Explorers into retreat before flying away. Inspired by the adventure he has had, Roy catches Hogator and gains his grandfather's permission to explore the world with the Rising Volteccers to catch Rayquaza. Meanwhile, the Explorers' leader, Gibeon, removes Amethio from his mission in favor of his teammate Spinel, leaving Amethio to pursue Rayquaza to determine its connection to the pendant.

Unwilling to leave Hogator, Roy stows aboard the Brave Asagi to become its partner. The crew allows Roy to stay the night, but he is unable to find Hogator and returns home the next morning. Hogator learns of Roy's visit and goes looking for him, discovering along the way that the Explorers have followed the Rising Volteccers. Reuniting with Hogator and warned about the Explorers, Roy enlists the local bug Pokémon to patch the Brave Asagi's balloon, while Friede and the rest of the crew battle Amethio and Zir to protect the ship. Roy joins the battle and motivates Hogator to perform its first successful Ember attack, but their achievement distracts Friede and allows Amethio to move in on Liko.

The Rising Volteccers dock at Roy's island to repair the damaged Brave Asagi. Their Hogator stumbles overboard and wanders through the island's forest, eating a stash of berries it finds before being discovered by Roy, who befriends it. Liko and Nyahoja notice Hogator's absence and track it to the forest, where they are attacked by wild Pokémon that blame them for eating the berries. The two are aided by Roy, who owns an ancient Poké Ball that resonates with Liko's pendant, but the group and Hogator are quickly ensnared by the wild Pokémon. Friede rescues the group and calms the wild Pokémon, which forgive Hogator after Liko and Roy help it replace the berries. Liko, Nyahoja and Hogator part with Roy before returning to the repaired Brave Asagi.

The day after Nyahoja's disappearance, Friede traces the Explorers to a nearby port town, and the crew agrees to help Liko take back Nyahoja. Conia, who has been affectionately caring for the captive Nyahoja, is sniffed out by Murdock's Iwanko at the Pokémon Center. The gang gives chase, and Amethio orders Conia to lure them to their hideout. There, Friede stalls Amethio in a battle to allow Liko to go rescue Nyahoja. Confronted by Conia outside, Liko commands Nyahoja to use Leafage in order to make their escape in the flurry of leaves. Friede notices his plan succeeded and retreats. The Rising Volteccers and Liko regroup and set sail for her home in Paldea. Meanwhile, a local islander named Roy chances upon the Brave Asagi's missing flag on the beach.

Liko, now encased in a green sphere, sees a strange Pokémon, which disappears moments later. Friede, the man with the Lizardon, takes Liko away from danger and brings her to an airship known as the Brave Asagi. Liko meets Friede's other companions and begins to trust them. Meanwhile, Amethio and his crew continues their pursuit of Liko's pendant and arrives on the airship. After a heated battle between Friede and Amethio, Liko's Nyahoja is blown off the airship. Amethio and his team decides to retreat, taking Nyahoja with them.

Liko, a shy girl from the Paldea region arrives in Kanto to begin her studies at the Indigo Academy. Eventually, Liko selects Nyahoja as her first Pokémon, but the two of them struggle to see eye to eye. One night, Liko encounters a man named Amethio, who hands her a letter that is supposedly from her grandmother, requesting her to bring her special pendant. Liko, feeling that the situation seems suspicious, decides to run away instead. While being pursued by Amethio and his crew, another man with a Lizardon comes to Liko's rescue. When Liko attempts to jump, her pendant begins to glow.