Balto (voiced by Maurice LaMarche) and his mate Jenna (voiced by Jodi Benson) have a new family of six puppies. Five of their puppies look like their husky mother, while one pup named Aleu (voiced by Lacey Chabert) clearly 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. Aleu stays with her father, Balto. A year later, after she is almost killed by a hunter (voiced by Joe Alaskey), Balto tells Aleu the truth about her wolf heritage. In anger and sadness, she runs away, hoping to find her place in the world.
At the same time, Balto has been struggling with strange dreams of a raven and a pack of wolves. He cannot understand what the dreams mean, but when Aleu doesn't come back the next day, he runs off to find her and bring her back home. He meets with mysterious creatures, like a cunning fox (voiced by Mary Kay Bergman), a trio of wolverines (voiced by Kevin Schon, Rob Paulsen, and Mary Kay Bergman) that taunt him, the same guiding raven from his dreams, and a furious grizzly bear that suddenly disappears as if it was never there.
During the journey, his friends Boris (voiced by Charles Fleischer), a Russian snow goose, and Muk and Luk (both voiced by Kevin Schon), twin polar bears, hope to find Balto, but they are halted by some unknown force. They soon realize that this journey to find Aleu is meant for the father and daughter themselves. Aleu, after taking refuge in a cave, meets the field mouse called Muru (voiced by Peter MacNicol) who lets Aleu realize that being part-wolf isn't so bad. He teaches her that everyone has a spirit guide. After singing the song "Who are you?", it turns out that Muru is Aleu's spirit guide.
When Aleu and Balto reunite after a close escape from the bear, a part that helped them escape is a strange ability that Aleu managed to get somehow, and allowed Aleu see the bear's thoughts. Aleu has started to grow, telling her father that she's not going home until she finds out who she is. The two of them travel onward, both following the raven, to a starving pack of wolves by the ocean. They are led by an old wolf named Nava (voiced by David Carradine), who has magic powers and can contact the mysterious white wolf, Aniu (voiced by Moonae Michael), 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 (voiced by Mark Hamill), a young wolf, 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 (voiced by Joe Alaskey), Yak (voiced by Jeff Bennett), and Sumac (voiced by Rob Paulsen).
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 realize that the pack is floating away, leaderless. Nava cannot make the swim in his old age, and Niju shows his fearfulness when Balto tells him to swim across to the pack and returns to his homeland. Balto is prepared to help the pack, but Aleu realizes that this is where she truly belongs. 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