Willy the whale is back, this time threatened by illegal whalers making money off sushi. Jesse, now 16, has taken a job on an orca-researching ship, along with old friend Randolph and a sarcastic scientist, Drew. On the whaler's ship is captain John Wesley and his son, Max, who isn't really pleased about his father's job, but doesn't have the gut to say so. Along the way, Willy reunites with Jesse
Main Title — Cliff Eidelman
Opening credits. Max stops by the store and then heads home.
China Grove — The Doobie Brothers
Jesse briefly gets distracted by the girls looking at him during his drive to the marina.
Harpoon Assembly — Cliff Eidelman
Max watches John prep the harpoons.
Awakening — Cliff Eidelman
One whale gets shot. John attempts to shoot Willy, but the captain's steering caused Max to go overboard. Max encounters Willy.
Willy Signals — Cliff Eidelman
Jesse and Randolph discover the whalers who shot Willy. Willy confronts John.
Whale Call — Cliff Eidelman
Jesse explains to Max how the whales sing. Willy greets the boys.
What Do You See? — The Skydiggers
Despite Randolph's concern, Jesse continues investigating Botany Bay and suggests coming up with another idea to prevent John from leaving. Randolph pretends to be drunk in front of John.
Big Sky — Reverend Horton Heat
Randolph triggers a fight against John and his crew.
Pressin' On — Little Charlie & The Nightcats
Jesse, after revealing the evidence, tries to warn Drake that Botany Bay's going after the whales right now. Unfortunately, Drake instead plans to call help in the morning.
The Hunt — Cliff Eidelman
Max confronts his father for killing the whales. Jesse, Randolph and Drew locate Botany Bay. Max jumps into the water to secretly give Jesse time to catch up.
Obsession — Cliff Eidelman
Randolph helps Drew with making a call to Botany Bay. Jesse saves Willy by crashing the Noah into Botany Bay which in-turn knocks John into the water.
Redemption — Cliff Eidelman
Jesse and Max convince Willy not to kill John who tries to kill him. Willy ends up sparing John.
You Were Right — Cliff Eidelman
Max and John have a heart to heart.
Birth — Cliff Eidelman
Jesse and Randolph film Nicky going into labor.
A New Family — Cliff Eidelman
Jesse, Max and Randolph discuss naming the newborn orca. Max picked Willy's name while Jesse picked Max's name. Willy, Nicky and Max swim happily as a family.
End Credits — Cliff Eidelman