Off the Pacific Northwest coast, two crews set out in search of killer whales, but for completely different reasons. Jesse is back, and he's now working for a NOAA research ship with his friend and mentor Randolph. Using Jesse's modified harmonica sound, they are successful in attracting Willy and his new pod. This is bad, however, because a whaling crew headed by John Wesley, is hunting for whales in the area. After John gets a hold of the harmonic signal and threatens to kill Willy and the other whales, Jesse realizes that he must fight to free Willy once again.