On a new day in the Kanto region, Satoshi gets invited by Professor Yukinari Ookido over to Professor Sakuragi's lab-opening ceremony in Vermillion City. During the ceremonial speech, Professor Sakuragi receives an alert of a possibly rare Pokémon appearing in Vermillion City's harbor, leading Satoshi and the other trainers to rush to the area in hopes of finding the mysterious Pokémon. At the harbor, they find Lugia—a Legendary Pokémon—engaged in combat with other trainers. Noticing the other trainers' tactics, Satoshi has his partner, Pikachu, strike Lugia with a Thunderbolt attack. Unfazed, Lugia flees, but not before Satoshi determinedly leaps onto its back. To Satoshi's surprise, he meets another boy, Gou, who leapt onto Lugia's back as well. The two ride on Lugia's back as it brings them along on a bizarre adventure across the seas. As it lets the two back on the ground, Satoshi and Gou bid their farewells to Lugia and return to Sakuragi Institute. Impressed by Gou's findings and Satoshi's insight taken during their encounter, Sakuragi requests for the duo to be his new research partners. And so the duo's journey begins, traveling across multiple regions to meet many new Pokémon—including ones that have the ability to Gigantamax!

Pokémon are peculiar creatures with a vast array of different abilities and appearances; many people, known as Pokémon trainers, capture and train them, often with the intent of battling others. Young Satoshi has not only dreamed of becoming a Pokémon trainer but also a Pokémon Master, and on the arrival of his 10th birthday, he finally has a chance to make that dream a reality. Unfortunately for him, all three Pokémon available to beginning trainers have already been claimed and only Pikachu, a rebellious Electric-type Pokémon, remains. However, this chance encounter would mark the start of a lifelong friendship and an epic adventure! Setting off on a journey to become the very best, Satoshi and Pikachu travel across beautiful, sprawling regions with their friends Kasumi, a Water-type trainer, and Takeshi, a Rock-type trainer. But danger lurks around every corner. The infamous Team Rocket is always nearby, seeking to steal powerful Pokémon through nefarious schemes. It'll be up to Satoshi and his friends to thwart their efforts as he also strives to earn the eight Pokémon Gym Badges he'll need to challenge the Pokémon League, and eventually claim the title of Pokémon Master.

Satoshi, Iris and Dent continue their travels through the Isshu region. After successfully winning his eighth Gym Badge against Homika in Tachiwaki City, Shirona invites everyone to stay at her villa in east Isshu, where old friend Hikari is also staying, and participate in the Pokémon World Tournament Junior Cup before Satoshi participates in the Isshu League. Team Rocket, meanwhile, initiate their final plan for the Isshu region. What is the purpose of their desire for the legendary Pokémon Meloetta?

By embracing challenges, learning from failures, overcoming obstacles, and beating the best in the world, Satoshi finally achieves his long-held dream. His adventurous spirit, however, still runs high as he continues to explore new regions, witness unfamiliar Pokémon, and forge unexpected friendships and rivalries. As the world opens its vast horizons to Satoshi, he once more encounters the people who helped shape his momentous path to success. A legendary journey nears its end just as an entirely new one is about to begin, with the bond between humans and Pokémon continuing forevermore.