Satoshi, a ten-year-old aspiring Pokémon Master from Pallet Town, oversleeps on the day he is to receive his first Pokémon from Professor Okido. Arriving late, he receives Pikachu instead of a standard starter. Pikachu proves volatile and disobedient, refusing its Poké Ball and resisting commands. Their relationship remains contentious during early encounters, like a confrontation with a wild Pidgey.

The dynamic shifts dramatically when a flock of Spearow attacks. Satoshi shields Pikachu with his body, prompting Pikachu to unleash a powerful Thunderbolt, driving the Spearow away. This act forges a strong bond. After the storm, the Legendary Pokémon Ho-Oh appears overhead, dropping a Rainbow Wing feather. Witnessing Ho-Oh inspires them to journey to Mount Tensei to find it, driven by the prophecy that the holder of the Rainbow Wing—the "Rainbow Hero"—is destined to meet Ho-Oh.

Satoshi demonstrates notable competence early on, strategically capturing a Caterpie after weakening it with Pikachu. He teaches Pikachu the move Iron Tail. Satoshi earns multiple Gym Badges, including a legitimate victory over Celadon City Gym Leader Erika for the Rainbow Badge. His Caterpie evolves into Metapod and later Butterfree. He rescues an abandoned Charmander deemed too weak by its Trainer, Cross, nurses it back to health, and it willingly joins his team, eventually evolving into Charmeleon and later Charizard.

Traveling companions join Satoshi: Verity, a skilled Trainer from Sinnoh using a Piplup, and Sorrel, an aspiring Pokémon researcher accompanied by a Lucario. Sorrel shares a tragic backstory of losing his Luxray in a snowstorm, making him initially hesitant to bond deeply with Pokémon. The group encounters Legendary Pokémon Entei, Suicune, and Raikou while following the glowing Rainbow Wing's guidance to Mount Tensei. They release Satoshi's Butterfree so it can migrate with a mate, a decision made with sadness but acceptance.

Conflict arises when Cross reappears, defeating Satoshi's Charmeleon with his Incineroar. Humiliated and frustrated, Satoshi expresses regret about choosing Pikachu, wishing for Squirtle or Bulbasaur. This doubt and ingratitude cause the Rainbow Wing to lose its color. The Mythical Pokémon Marshadow, guardian of the Wing, subjects Satoshi to a dreamlike state where he exists in a world without Pokémon, attending school with Verity and Sorrel. Realizing Pikachu's absence jolts Satoshi back, restoring the Wing's color and prompting reconciliation with Pikachu.

At Mount Tensei, Cross confronts them again, seeking Ho-Oh. After his Incineroar is defeated by Satoshi's Charizard, Cross steals the Rainbow Wing. His corrupted intent darkens the Wing, prompting Marshadow to possess nearby Pokémon, including Cross's Lycanroc, turning them aggressive. To protect a weakened Pikachu from the attack, Satoshi recalls it into its Poké Ball—a rare containment—and is seemingly disintegrated by energy blasts. Witnessing Satoshi's apparent death, Pikachu unleashes a grief-fueled Thunderbolt, dispelling Marshadow's influence and reviving Satoshi. Satoshi places the restored Rainbow Wing on the Rainbow Rock, summoning Ho-Oh. He challenges Ho-Oh to a battle with Pikachu. Ho-Oh heals the group before departing.

After encountering Ho-Oh, the companions part ways: Verity returns home, Sorrel pursues research on Legendary Pokémon, and Cross departs peacefully with his Pokémon. Satoshi and Pikachu continue their journey alone. A subsequent special episode, "The Distant Blue Sky," reveals more of Satoshi's family: his father is present but they often miss each other due to conflicting travels. His father gifts him his iconic hat. During this special, Satoshi experiences an unexplained moment of emotional vulnerability, shedding tears while eating, potentially linked to his father's absence.