Kallik is a polar bear that lives with her mother and her brother. They are safe and secure in their winter den, but Kallik is worried that they will not be able to find food when summer comes and they can no longer hunt seals. Her mother tells the cubs about a faraway land where the ice never melts and the food is always abundant. Later, Kallik falls through some broken ice. Her mother saves her from drowning in the cold water below, but her mother realizes that the broken ice means that the warm season is arriving soon.
Lusa is a black bear that lives in the Bear Bowl, the bears-only section of a zoo. She enjoys the attention she receives from the crowds at the zoo, but she longs to be free and live in the wilderness. Lusa begins asking her father, King, about life in the wilderness. King insists that his daughter will never live outside the zoo, so she does not need to keep asking him questions.
Toklo, a grizzly bear, lives in the forest with his mother, Oka, and his brother, Tobi. Tobi is a sickly bear, and Toklo must work hard to find extra food for his weaker brother. Oka decides to take her cubs over the dangerous mountains to reach a salmon stream that is supposed to have an abundance of food. They travel over the mountains to find more food, but the journey is difficult and Toklo's brother dies.
While Kallik and her family swim through the icy water, orca whales attack them. Kallik is separated from her mother and her brother. After they are separated, Kallik believes that her mother is dead. She begins to look for her brother. Exhausted and hungry, she eventually comes to the end of the ice and reaches land. Kallik begins to explore the dry land for the first time. Kallik sees other polar bears walking in the same direction, and she remembers that her mother mentioned a special gathering place for polar bears on land. She follows the other bears in hopes of finding her brother. Then she follows the bright Pathway Star, hoping it will lead her to the meeting place of the polar bears. Eventually, she finds the polar bear gathering place.
Oka performs a funeral ritual for her son by piling moss and leaves on his body. Oka and Toklo travel to a river where many bears are catching fish. Oka wanders away from Toklo, saying that she can't stand to watch her cubs die. Toklo watches his mother have an emotional breakdown. She talks to herself and threatens other bears when they come near her. Oka chases Toklo away, saying that she has no cubs anymore.
Lusa's mother falls sick. The zookeepers take her away, and Lusa does not understand why — she does not know they are giving her medicine. Eventually, Lusa's mother returns. Lusa's first springtime arrives, and a new grizzly bear is brought to the zoo. The new bear is Oka, Toklo's mother. Oka is still raving with grief, but Lusa still tries to make friends with her. Lusa enjoys Oka's stories about the wilderness. Lusa's father does not want Lusa to listen to these stories or think about life outside the zoo. One day, Oka attacks a human attendant who is trying to feed her. The zookeeper is taken to the hospital, and Oka is tranquilized. When Oka wakes up, Lusa promises to go into the wild and find Toklo for her. Since Oka is so worried about him, Lusa promises to protect Toklo.
Toklo has trouble living on his own in the wilderness. He digs up other bears' stashes of food and eats the garbage from trash bags humans have left behind. He overhears another mother bear telling her two cubs how to catch salmon. Toklo steals a fish from the two younger bears before their mother chases him away.
Kallik discovers that all of the other polar bears at the gathering place are tired, hungry and hopeless. She journeys toward some human houses in hopes of finding her brother.
Lusa wants to escape from the zoo to find Toklo and protect him. King explains to Lusa that it would be nearly impossible for her to feed herself in the wild. In addition to the scarcity of food, he mentions the danger presented by other bears that might attack a defenseless cub like Lusa. Lusa still wants to leave; she stops eating her food and pretends to be sick so the zookeepers will take her out of her cage and give her a chance to run away. When the zookeepers remove her from her enclosure, Lusa manages to free herself and climb over the large chain link fence that surrounds the zoo.
Toklo sees some human hunters chasing another bear cub. They poke the cub with sticks, throw rocks at it and finally shoot the cub in the shoulder. Toklo helps the wounded cub run away from the hunters and their dogs. The two cubs find refuge in a small cave. Toklo is shocked when the wounded cub transforms into a human boy named Ujurak who can speak the language of bears.
Toklo discovers that Urjurak is a shape shifter. Ujurak needs Toklo to find a special herb so he can heal the wound on his shoulder. Ujurak treats his own shoulder wound with a paste made from the herb, and he also puts the paste on Toklo's scratch. Toklo catches his first salmon in a river, and he again meets Ujurak in bear cub form. Ujurak says he is not sure whether he is a bear or a boy, because he changes form so often. Toklo agrees to travel with Ujurak.
Kallik enters a human neighborhood and is shot with a tranquilizer when she enters a house and steals food. She is taken to an enclosure where polar bears are brought when they venture too close to human houses. Another bear tells her that she will be released into the wild again. A female bear named Nanuk offers to take care of Kallik, even though Kallik is not her cub. Kallik falls asleep in her cage, snuggled against Nanuk.
Lusa walks through the forest for the first time, and has difficulty finding food. She discovers a bee tree and fills her stomach with honey. Lusa soon meets an aggressive grizzly bear. Lusa climbs a tree to get away from the angry grizzly bear. After he goes away, she continues her journey to find Toklo.
Toklo and Ujurak keep traveling. Ujurak sees a blackbird and then transforms himself into a blackbird. Ujurak turns into a cub again and tells Toklo that he cannot control his transformations — they happen when he is excited or frightened. When they come near a salmon stream, Ujurak turns into a salmon, and Toklo has to try to keep other grizzly bears from eating him. Toklo is so upset by the incident, he tries to leave Ujurak behind, but he finds that he cannot abandon the helpless shape-shifting cub.
Kallik and Nanuk are tranquilized and then taken to a helicopter that will transport them to where they will be released into the wild. The helicopter crashes, injuring Nanuk. As Nanuk dies, she tells Kallik to travel to the place of endless ice, where she will be safe.
Toklo and Ujurak look for food. Ujurak controls his transformation for the first time, briefly turning into an eagle and killing a goat for the two of them to eat. Then Ujurak turns into a rabbit and is nearly killed by a young black bear. The black bear turns out to be Lusa, who is thrilled to finally meet Toklo.