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.

The millions of Keiko fans around the world finally learn the truth about what really happened when the Free Willy star became the first and only captive orca to be released back into the wild. The most unlikely candidate for release because of his long years in captivity, actually thrived for over 5 years in his home waters, gaining over 3000 lbs during his rehabilitation, mixing it up with wild orcas, swimming across the North Atlantic, and finally passing as a middle aged orca as the only captive orca to ever be successfully rehabilitated and released back to to the 'wild' - come join Keiko's Pod and help Rescue Rehab and Release all of the other whales and dolphins currently in captivity.

Many years ago, aliens released Keiko the killer whale on Earth. Since then he has spent most of his life in a water park and has taken the love from their caregivers and the public. Everything will change when the aliens come back for her.