Brother and younger sister-in-law live in the house which parents are often away from. Yuki who is the younger sister is secretly yearning for Kenji who is the elder brother. However, one girl came to show up from the closet in Kenji's room after a certain night. Moreover, her body is transparent, and she looks like the ghost. Her name is Hiyori. She is a friend in their childhood. They are pleased with reunion though Kenji and Yuki are perplexed with the way of Hiyori's strange appearance. However, Yuki gets the mind shaken as Kenji and Hiyori become intimate, and the pain in her mind in the childhood is recalled. At the childhood, Yuki was going to pass the light blue toy ring which Kenji had had to Hiyori in exchange for Hiyori's yoyo. However, because Hiyori became sick, and had moved, the promise was not an accomplishment. Their events in the childhood seem to be related to Hiyori's showing up in front of them. A painful love story of Kenji and two girls progresses.

The story revolves around a race that seeks to dominate the galaxy. A lone mysterious female warrior, known to others as Emeraldas sails the endless planets of the universe- in her Seas of Star ship- fighting the tyranny of that merciless race. She is tormented by the memory of her lost love.

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!