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!

Ichiro Hanada is a hyperactive little boy who lives with his parents, sister, and grandfather in a rural town. He is always up to some kind of mischief, often teasing his sister or making rude comments to others. Consequently, his mother constantly scolds him, and even the neighbours express disturbance from time to time on how rowdy he can be. One day, after pulling a terrible prank, Ichiro sprints onto the streets as his mother chases him. He steals a nearby bicycle and takes on a dangerous route, eventually being hit by a truck. Miraculously, he survives the crash, requiring nine stitches to the back of his head and balding for the surgery. However, the near-death experience gains him the ability to see ghosts—the last thing he needs in his life. Since Ichiro is the only one who can communicate with them, several ghosts of people who have recently died come to him, seeking help to fulfill their last wishes before achieving enlightenment. Each adventure with a ghost leaves the young and curious boy with a different lesson that gradually makes him wiser.

Self-professed "home security guard" Mahiro Oyama has not left his home in years, secluding himself in his room playing erotic visual novels. This depraved lifestyle causes his prodigious sister, Mihari, to worry about his well-being. In hopes of solving this problem, she devises a plan to rehabilitate him back to normalcy. The first part of Mihari's plan is to concoct a medicine that changes her brother's biological constitution into a bona fide female, much to Mahiro's vehement dismay. Stuck in this predicament, Mahiro has no choice but to live out his life as a cute girl until the effect wears off—if it ever does.

Self-professed "home security guard" Mahiro Oyama has not left his home in years, secluding himself in his room playing erotic visual novels. This depraved lifestyle causes his prodigious sister, Mihari, to worry about his well-being. In hopes of solving this problem, she devises a plan to rehabilitate him back to normalcy. The first part of Mihari's plan is to concoct a medicine that changes her brother's biological constitution into a bona fide female, much to Mahiro's vehement dismay. Stuck in this predicament, Mahiro has no choice but to live out his life as a cute girl until the effect wears off—if it ever does.