The film begins with a pod of orcas swimming near the coastline of the Pacific Northwest. The pod is tracked down by a large group of whalers, and one of them, Willy (Keiko the orca), is snared in their nets and taken away to a local amusement park.

Sometime later in Astoria, Oregon, Jesse (Jason James Richter), a troublesome 12-year-old boy who has been on the streets since he was abandoned by his mother six years before, gets caught by the police for stealing food and vandalizing a theme park. Jesse's social worker Dwight earns him a reprieve by finding him a foster home and having him clean...