Winnie the Pooh, Piglet, Tigger, Rabbit, Eeyore, Christopher Robin, Bloom, Stella, Flora, Musa, Tecna, Layla, The Vultures, Jiminy Cricket, and Zazu bring Kanga, Roo, Lumpy, Darby, Buster, Alvin, Simon, and Theodore Bloom to Nome, Alaska to reunite with Balto and his mate Jenna, who have a new family of six puppies. Five of their puppies look like their husky mother, while one pup named Aleu 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, 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 and he cannot understand their meaning. 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, a trio of wolverines 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, 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 for the father and daughter themselves.
Aleu, after taking refuge in a cave, meets the field mouse called Muru 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, Aleu realizes she has gained a strange ability that allowed her to 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, 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), whom The Trix and Hades work for, 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.
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, 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. 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.
- Christopher Robin, Kanga, Roo, Lumpy, Darby, Buster, Bloom, Stella, Flora, Musa, Tecna, Layla, Roxy, Lumiere, Cogsworth, Mrs. Potts, Chip, Scuttle, Frosty the Snowman, Jaq and Gus, Vanellope von Schweetz, Will Vandom, Irma Lair, Taranee Cook, Cornelia Hale, Hay Lin, Napoleon (W.I.T.C.H.), Alvin Seville, Simon Seville, Theodore Seville, The Vultures, Jiminy Cricket, Zazu, The Trix (Winx Club) (Icy, Darcy, Stormy), and Hades guest star in this film.
- This is an NTSC film with NTSC bits from the Winnie the Pooh films, the Alvin and the Chipmunks films, The Secret of NIMH 1 and 2, Winx Club: The Secret of the Lost Kingdom, Beauty and the Beast, The Little Mermaid films, the Cinderella films, Wreck-It Ralph, The Jungle Book 1 and 2, Pinocchio, Mickey's Christmas Carol, The Lion King films, and Hercules.
- Kanga, Roo, Lumpy, Darby, and Buster were originally planned to be absent from this film, which was originally set to be a prequel to Pooh's Adventures of Rudolph the Red-Nosed Reindeer: The Movie (due to Aleu guest starring in that film at first) and not feature guest stars (except Christopher Robin), but since all of Legoland1085's Pooh's Adventures films (including that film) will possibly be remade by different users with some changes, it was decided that Kanga, Roo, Lumpy, Darby, and Buster will be included and Yru17 decided to add Bloom and her friends, The Vultures, Jiminy Cricket, Zazu, and The Trix to this film.
- This film actually takes place after Bloom Meets Balto, which explains Balto and his friends already knowing Bloom and her friends, the Alfea Adventure Crew, The Vultures, Jiminy Cricket, and Zazu and facing The Trix.
- Yru17 originally requested RatiganRules to make Winx Club crosovers with the Balto sequels, but he wasn't interested in making any of them and Yru17 is aware that there are some films and TV shows RatiganRules doesn't plan to make Winx Club crossovers of. So the Winx Club characters ended up guest starring in the Winnie the Pooh/Balto sequels instead.
- Balto and his friends will face Hades again in Littlefoot's Adventures of Hercules.
- Alvin and the Chipmunks Meet Frankenstein, Alvin and the Chipmunks Meet the Wolfman, and Balto II: Wolf Quest were produced by Universal Animation Studios (formerly known as Universal Cartoon Studios).
- The story concludes in Winnie the Pooh and Bloom Meet Balto III: Wings of Change.