Serebii, a Legendary Pokémon known for its ability to traverse time, is hunted by an unnamed Pokémon poacher seeking to capture it. Yukinari, a young Pokémon trainer who enjoys drawing portraits of Pokémon, tries to protect Serebii after it stumbles upon him; but in the middle of its escape, both vanish without a trace. Forty years later, ambitious Pokémon trainer Satoshi hopes to sight rare Pokémon around his local area. White, a boat driver, takes Satoshi to his village. Satoshi is accompanied by his three closest friends: Takeshi, a former gym leader training to be a great Pokémon breeder; Kasumi, a young girl wanting to become a skilled Water-type trainer; and Pikachu, Satoshi's Pokémon partner and first comrade. Meanwhile, Yukinari and Serebii reappear in Satoshi's present time and run into his group. Masked Lord Vicious, the strongest executive staff member of Team Rocket, desires to capture Serebii. Using the Dark Ball, a variant of Monster Ball that corrupts the Pokémon caught within and draws out their maximum power, Vicious can transform innocent Pokémon into powerful and frightening obstacles—including Serebii itself! Placed in a tough position, Satoshi, Yukinari, and their friends must work together to defeat Vicious and save Serebii and themselves.

Following the end of Satoshi's Hoenn journey, he travels to the Sinnoh region for his next adventure en route to becoming a Pokémon Master. Immediately upon arrival, Team Rocket makes another attempt to snatch Pikachu, only for it to fail once again. However, Pikachu has fallen deep into a forest and it's up to Satoshi to find him! Along the way, he reunites with Takeshi—a Pokémon breeder with whom he has traveled through many regions—and meets his soon-to-be rival, Shinji, a power-hungry trainer who cares little for his Pokémons' feelings. Still in search for Pikachu, Satoshi notices a powerful electric attack in the distance and heads toward it to find Pikachu with Team Rocket and Hikari—a novice trainer aiming to be the top Pokémon coordinator. After foiling Team Rocket's plans, Satoshi reunites with Pikachu and Hikari joins the group. And thus, Satoshi and his friends begin their journey through the exciting land of Sinnoh.

High schooler Ganta Nakami has trouble falling asleep most nights. As a result, he is irritable at school, always searching for an opportunity to find a secluded place to doze off. On the other hand, Isaki Magari is a free spirit who is well liked by her friends, but no one is aware of her sleep disorder. She makes use of the school's abandoned astronomy club observatory as her secret sleeping bunker when she needs to get some shut-eye. As fate would have it, Nakami finds Magari napping in the observatory. When Magari discovers that she and Nakami have something in common, she offers to share her secret sleeping spot with her fellow insomniac. As the two find warmth in each other's company, the struggles they face start to become easier to confront.

On the beautiful banks of the Arakawa River, it is lively as ever. Now known as Recruit, Kou Ichinomiya has adjusted to the troubles his unconventional neighbors brew daily. However, the atypical scene is about to get even rowdier when their community adds a couple of oddball enthusiasts: a tall, muscular woman calling herself Amazoness, followed by her loyal Tengu henchmen; and Captain, self-proclaimed Commander of Earth's Defense Force against Venusians. In spite of all the commotion, Recruit gradually learns more about his lover Nino and the story that shaped her.