In the third instalment in the Free Willy series, a teenage Jesse and old friend Randolph try to foil an illegal whaler threatening Willy and his pregnant mate.
Jesse (Jason James Richter) is now 17 years old and has landed a summer job tracking whales on an oceanic research vessel with his old mentor, Randolph (August Schellenberg). Together they are trying to find the cause of a mysterious decline in the local Orca population in the remote waters off the rugged Northwest Pacific coast. On the verge of manhood, Jesse struggles to be taken seriously by the head research scientist Drew (Annie Corley) and the other adults on the scientific team. Meanwhile, Willy has also matured into a young adult and has taken the additional responsibility of a mate. Jesse befriends 10 year old Max (Vincent Berry), whose father John (Patrick Kilpatrick) runs a business of illegal whaling. Together they embark on a dangerous mission to save Willy and his pod.