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!

In the kingdom of Highland, fairies lived freely until humans betrayed them. Once a fairy has been stripped of a wing, whoever possesses it holds the fairy's life in their hands. Taking advantage of this, humans enslaved fairies, but 15-year-old Ann Halford longs to see the day when fairies and humans are treated as equals. The aspiring confectioner dreams of becoming a Silver Sugar Master just like her late mother. In order to achieve this lofty goal, Ann sets out for the capital of Lewiston, home to the annual Royal Candy Fair. However, to be bestowed the elusive title, Ann's confection crafted from silver sugar must be recognized with a royal medal at the event. Ann hires a sharp-tongued warrior fairy, Shall Fen Shall, to be her bodyguard for the perilous journey ahead. After saving him from his cruel fairy trader, she promises to return Shall's wing to him once they reach the capital, much to his confusion. But as the pair travel further along, the time they spend together grows, and they learn more about each other and their true desires.

In the world of Ars, humans lead a decades-long war against giant beasts that ravage the lands and feed on their resources. Those tasked with fighting them are champions called nagimori, who utilize the destructive power of kannagi: beings gifted with uncontrollable magical powers. While mourning the death of his war partner, former nagimori Jiiro crosses paths with Kuumi, a young woman who has just awakened her magical powers. After the pair form a contract to save the city from a giant beast attack, Jiiro learns that Kuumi has escaped a laboratory and is being hunted by the underlings of Mezami, the head of the research facility. Reluctantly agreeing to help Kuumi flee from her pursuers, Jiiro starts traveling with his new partner and her friend Myaa, a young girl with a cat headdress. As the unlikely trio wanders the Arsian lands, top officials begin setting their plans into motion—and the group of adventurers soon discover that men are to be feared more than monsters.

Sightings of mysterious creatures known as "Hologram Ghosts" have been a popular topic on social networks for the past few years. According to the rumors, several people have fallen victim to these specters. Those fortunate to survive their encounters with the paranormal beings claim that they resembled glitched holograms. Hazakura Academy middle school student Hiro Amanokawa believes these sightings are merely an urban legend. However, as the incidents start to increase in frequency, he is reminded of the day his father suddenly vanished, with strange digital watches serving as the only relics of his disappearance. Much like the other sightings, what happened to Hiro's father cannot be explained by conventional logic. One day, when a fellow student in the academy is attacked by a Hologram Ghost, Hiro and his friend Kiyoshirou Higashimitarai decide to look into the matter. Little does Hiro know that this investigation will be their first step toward discovering a dangerous world previously unknown to mankind.