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.
Meanwhile, a 10-year-old boy named Max Wesley (Vincent Berry) idolizes his father and wants to follow in his footsteps. But, his happiness turns to dismay when he is confronted with the reality of his father's true business -- illegal whaling. When Jesse subsequently meets and befriends Max, the two boys embark on an extremely dangerous mission to save Willy and his pod from death at the hands of Max's father. Along the way, young Max must find the courage to stand up to his father, and Jesse rediscovers the extraordinary strength of his bond with Willy.