Willy the Orca is threatened by illegal whalers poaching whales for fancy sushi. Jesse (Richter), now 16, has a job on a whale research ship, along with an attractive but iconoclastic scientist, Drew (Corley). Aboard ship, Captain John Wesley (Kilpatrick) struggles with son, Max (Berry), who isn't happy about his father's job (although he can't bring himself to say so). Along the way, Willy happily reunites with Jesse, and helps Max realize that whales are valuable as free, living creatures. Old friend Randolph, a Native American and friend both to Jesse and Willy, joins the adventure.