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The series primarily follows an orphan boy named Jesse who befriends a killer whale named Willy, and eventually develops a strong connection. While trying to juggle his newly found life, he and Willy are challenged with overcoming or defeating various hazards to the ocean or Willy himself including corporate greed, hunters, poachers and oil disasters.
When maladjusted orphan Jesse vandalizes a theme park, he is placed with foster parents and must work at the park to make amends. There he meets Willy, a young Orca whale who has been separated from his family. Sensing kinship, they form a bond and, with the help of kindly whale trainer Rae Lindley, develop a routine of tricks. However, greedy park owner Dial soon catches wind of the duo and makes plans to profit from them.
Jesse becomes reunited with Willy three years after the whale's jump to freedom as the teenager tries to rescue the killer whale and other orcas from an oil spill.
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.