Balto and his mate Jenna have a new family of six puppies in Alaska. Five of their puppies look like their husky mother, while one pup named Aleu takes her looks from her wolfdog father. When they all reach eight weeks old, all of the other pups are adopted to new homes, but no one wants Aleu due to her wild animal looks. Soon, she stays with her father. A year later when she grows up, after she is almost killed by a hunter, Balto tells Aleu the truth about her wolf heritage. In anger and sadness, she runs away, hoping to find her place in the world. Balto then goes out to find her.
At the same time, Balto has been struggling with strange dreams of a raven and a pack of wolves, and he cannot understand their meaning. While traveling to find Aleu, he hopes he'll find answers. He meets with mysterious creatures, like a cunning red fox, an intimidating trio of wolverines that taunt him, the same guiding raven from his dreams, and a furious grizzly bear that suddenly disappears.
During the journey, his friends Boris, Muk and Luk hope to find Balto, but they are halted by some unknown force. They soon realize that this journey to find Aleu is meant only for the father and daughter themselves.
Aleu, after taking refuge in a cave, meets a field mouse called Muru, who lets Aleu realise that being part-wolf isn't so bad. He teaches her that everyone has a spirit guide as soon as they are born, and their heritage tells them what they are but not who they are. After learning valuable lessons from the field mouse, Aleu realizes that Muru is her spirit guide. She asks him what to do, and he tells her to have confidence and to continue her journey with the wisdom he had given her. Eventually, Balto and Aleu reunite and forgive each other.
The two of them travel onward, and encounter a starving pack of wolves by the ocean, led by an old wolf named Nava, who has magic powers and can contact the mysterious white wolf, Aniu, in his "dream visions". He tells his pack that one day soon, they will be led by a new leader, "the one who is wolf but does not know". Everyone believes that Balto, who is half wolf himself, is the chosen one that Aniu was speaking of. However, Niju, a young wolf and member of Nava's pack, hopes that he will be the next leader since he is stronger and more powerful than the old, wise Nava. He plans to accomplish that with his followers Nuk, Yak and Sumac. During the night, the four wolves plot to get the pack to their side and to kill Nava, Aleu, and Balto.
The day comes to depart from their home to follow the caribou, the wolves' food source, across the large sea, using pieces of ice like a bridge, with Balto in the lead. When Nava is separated from the rest of the pack, Aleu joins him to help him across, but runs into Niju, who is ready to take the elderly leader's life and the young half-wolf's as well. Balto abandons the pack to save his daughter, but before anyone gets hurt, they realise that the pack is floating away, leaderless. Nava cannot make the swim in his old age, so Balto tells Niju to be their new leader and to swim across to the pack, but Niju refuses to leave his homeland. Balto is prepared to help the pack, but Aleu realizes that this is where she truly belongs. After saying goodbye to her father, she makes the swim to the pack to become its leader as Nava returns to his home to find Niju. As Balto makes his way back to Nome, the raven reveals its true form as the great white wolf, Aniu, who is Balto's mother.Maurice LaMarche as Balto
Jodi Benson as Jenna
Lacey Chabert as Aleu
David Carradine as Nava
Mark Hamill as Niju
Charles Fleischer as Boris
Peter MacNicol as Muru
Rob Paulsen as Terrier, Sumac, Wolverine #2
Nicolette Little as Dingo
Melanie Spore as Saba
Kevin Schon as Muk, Luk, Wolverine #1
Joe Alaskey as Hunter, Nuk
Monnae Michaell as Aniu
Mary Kay Bergman as Fox, Wolverine #3
Jeff Bennett as Yak
Frank Welker as The Grizzly Bear
Wolf Quest is one of the last movies Mary Kay Bergman contributed to before she committed suicide in November 1999.
Balto II: Wolf Quest was nominated for an Annie Award in 2003 for "Outstanding Storyboarding in an Animated Television Production".
Writer Dev Ross was awarded the Humanitas Prize in 2002 for his script in the Children's Animation category.