Kasumi and Takeshi both leave the group and return home. Satoshi returns to Masara Town and runs into Shigeru, who asks him how much closer he is to becoming a Pokémon Master. Meanwhile, the Team Rocket trio reunites and attempts to steal Pikachu again, only to have their plans foiled by Satoshi's Pidgeot. Later on, Satoshi decides that he wants to go on more adventures and meet many more Pokémon on his quest to become a Pokémon Master.

Satoshi and his friends rescue Latias and Latios from being pursued by a Pokémon hunter.

The Team Rocket trio are given back the Pokémon that they had acquired from their adventures from Sakaki. With all of their Pokémon together, they launch a mission to steal Pikachu once and for all. The trio's plan initially goes well, until the Latias that Satoshi had met earlier, sends Team Rocket blasting off. After failing to steal Pikachu again, the trio blames each other for their failures and go their separate ways. After, Latias suddenly shows Satoshi and the others a vision of a Latios that is in danger.

Satoshi, Kasumi, and Takeshi arrive in a town where heart-shaped objects are being taken from the town's residents by a Juppeta. The group discovers that Juppeta's motive for taking the items is because it used to wear a heart-shaped hair tie, which was gifted to it by its long-lost owner many years prior. Satoshi and his friends manage to reunite Juppeta with its owner, which turns out to be the local Nurse Joy.

Satoshi reunites with his Laplace that he had met on the Orange Islands. Laplace leads Satoshi and his friends over to an island where a Hoeruko is trapped in a hole. The group manages to free Hoeruko, and again after it had evolved into a Whaloh. Eventually, Satoshi becomes trapped in a cave before being rescued by Laplace. At sunset, Laplace says its goodbyes to Satoshi once again and returns to its herd.

While Satoshi and his friends are taking a break, Team Rocket suddenly appears and unsuccessfully steals Pikachu. The trio is sent blasting off along with Pikachu, but him and Nyarth become separated from their respective groups and are forced to work with each other to find Satoshi and Team Rocket.

Satoshi and his friends reunite with his Zenigame and the rest of its firefighting squad. Zenigame mistakes Satoshi for not caring about it and becomes upset with its trainer. However, after saving the day by extinguishing a nearby fire with Satoshi, Fushigidane, and Lizardon, Zenigame reconciles with its friends.

Satoshi, Kasumi, and Takeshi encounter a Tunbear that is unable to control its powers. Satoshi aids Tunbear and successfully teaches it how to use its moves effectively.

Satoshi and Kasumi travel to Galar and reunite with Takeshi and Dent. When Takeshi becomes heartbroken again, a wild Brimuon begins to play with his emotions. After Takeshi is rescued, he decides to rejoin Satoshi and Kasumi.

Satoshi arrives at a seashore and encounters an Udeppou. Before he can catch it though, Kasumi, one of Satoshi's old traveling partners, declares that she'll be the one to catch it. Satoshi and Kasumi have a Pokémon battle to decide who gets to catch Udeppou, with the battle ending in Kasumi 's favor. Later on, Kasumi decides to travel with Satoshi again.

While spending time out in the countryside, Satoshi comes across an injured Latias and helps it recover. Latias is initially skeptical of Satoshi, but after he rescues it from being captured by Team Rocket, Satoshi gains the trust of Latias.

Set in the same continuity as I Choose You, The Power of Us, and Secrets of the Jungle instead of the anime TV series, Satoshi and Pikachu continue their adventure as they help out a boy named Haruto.

Following their Raid Battle with Lugia, Satoshi and Go go their separate ways and embark on their new journeys.

Satoshi and Go return to Kanto and reveal their intentions on starting new adventures without each other. However, Go is unwilling to tell Satoshi his plan, as he doesn't want to betray his friendship with him. When Satoshi publicly announces his decision to continue his journey alone, Go becomes upset due to the feeling of betrayal. The dispute between the two friends is paused when Lugia suddenly appears, prompting Satoshi and Go to begin a raid battle with it.

The members of Project Mew are forced to confront Groudon and Kyogre. Mew reveals itself after disguising itself as the Hoenn Legendaries. Mew launches attacks at the Project Mew team until Go thanks it for inspiring him to set off on his journey. After the Project Mew team has achieved its goal, Go, Tokio, and Shigeru all go their separate ways.

The Project Mew team sets out for Faraway Island to commence their search for Mew. After being separated into two different groups, Shigeru and Tsurugi encounter a Groudon, while Go, Tokio, and Asahi come across a Kyogre.

Satoshi and Dande have their Daimax Bands recharged by Mugendina, leading to a battle between Kyodaimax Aceburn and Kyodaimax Pikachu, which ends in Pikachu's favor. Pikachu then goes up against Dande's Lizardon and briefly passes out. However, Pikachu becomes motivated after imagining all of Satoshi's Pokémon cheering for him, allowing him to get back up and deliver one last Thunderbolt on Lizardon. Pikachu manages to defeat Lizardon, resulting in Satoshi's victory over Dande. Satoshi becomes the new World Champion.

After Dande's Drapult is defeated, Dande gains some momentum and begins to turn the tables. Satoshi's Kairyu is taken down by the opposing Gorirander, who is then knocked out by Uonoragon. However, Uonoragon is beaten by Dande's Aceburn moments later. With just one Pokémon remaining, Satoshi sends in Pikachu to go up against Lizardon. After each Pokémon uses their strongest attacks, the clash causes Mugendina to reawaken and interfere with the heated battle.

Satoshi and Dande continue their battle, with Satoshi's Mega Lucario defeating Barrikohru. As the battle goes on, Dande's strategy begins to tease Satoshi. After Mega Lucario is knocked out by Drapult, Kairyu avenges its teammate by finishing off Drapult with a Draco Meteor, giving Satoshi a 3–2 lead. For his next Pokémon, Dande brings out his Gorirander.

Go travels to Hoenn for his next assignment for Project Mew. Meanwhile, Satoshi and Dande begin their full battle in the Masters Eight Tournament Finals, with Satoshi being allowed to use Mega Evolution, Z-moves and Daimax. In the battle, Gangar takes down Dande's Intereon, but Gangar is later knocked out by the opposing Barrikohru.

The battles from the Masters Eight Tournament semifinals and the teams for Satoshi and Dande are reviewed.

Go reunites with his Mugendina and chooses to leave it under Dande's care. Afterwards, Satoshi and Go revisit the place where Go had first met his Aceburn, leading them to reconnect with Aceburn's former friends. After a confrontation with Team Rocket, Go is summoned by Project Mew, forcing him to miss Satoshi's battle with Dande.