Sacha, a Pokémon Trainer from Pallet Town in the Kanto region, encounters Koko during a visit to the Forest of Okoya. After witnessing Koko plunge from a waterfall following an accident with a Skwovet and a vine swing, Sacha retrieves him from the water and rushes him to a Pokémon Center in nearby Milyfa Town for treatment. Koko, raised in isolation by Zarude, possesses no prior exposure to humans or their facilities.

Awakening in panic due to his unfamiliarity with humans, Koko flees the Pokémon Center. Recognizing Koko's unique upbringing and self-identification as a Pokémon, Sacha and his Pikachu patiently introduce him to aspects of human society within Milyfa Town, guiding him through the town and helping him acclimate to human customs and environments.

Sacha later accompanies Koko during an encounter with Zarude, Koko's adoptive parent, where Zarude reveals Koko's human origins. Discovering a Biotope Company wallet, Sacha takes Koko to the company's headquarters. There, Dr. Zed discloses information about Koko's deceased human parents and scans Koko's pendant, revealing corrupted data pointing to the Great Tree's location.

When Dr. Zed threatens the Forest of Okoya with a mechanized assault targeting the Great Tree, Sacha and Koko race to stop him. They are restrained by Dr. Zed's Ariados and confined in a truck. After escaping with inadvertent aid from Team Rocket, Sacha, Pikachu, and Koko confront Dr. Zed. During the ensuing battle, Sacha fights alongside Koko and the assembled Pokémon against Dr. Zed's giant tank. Koko ultimately unleashes the jungle's power to heal a critically injured Zarude, contributing to the tank's disabling and Dr. Zed's capture.

In the aftermath, Sacha departs the Forest of Okoya alongside Koko. He observes Koko's decision to explore the human world and embrace his dual identity as both human and Zarude, witnessing Zarude's symbolic farewell in the healing springs.