ate (Hayden Panettiere) and Humphrey (Justin Long) are two wolves from the same pack in Canada’s Jasper National Park but on opposite ends of the social order. Kate, daughter of the main alpha male Winston (Danny Glover) and his mate Eve (Vicki Lewis), is herself an Alpha and does what one should: taking her duty and commitment to the pack seriously. Humphrey, on the other hand, is an Omega wolf, the lowest of the pack, and spends his days making jokes and playing about with his other Omega friends Shakey (Kevin Sussman), Salty (Brian Donovan), and Mooch (Eric Price). Despite his low rank in the pack, Humphrey has a crush on Kate and he also nevertheless is valued in the pack as a peacemaker by virtue of his affable nature.
During youth, Kate left to begin Alpha school with her father. She returns as a fully trained Alpha but on her first hunt, two members of the Eastern pack ruin her attempt, leaving her pack with nothing but bones and scraps. Her pack and the Eastern pack have had a bitter rivalry since Winston dislikes the fact that Tony (Dennis Hopper), the Alpha male of the Eastern pack wants to unite into one large pack. Winston and Tony meet up one night and arrange for Kate to marry Tony’s son Garth (Chris Carmack). Kate had followed her father and heard everything. Kate wearily agrees for the good of the pack and she meets Garth at the Howling Rock. Humphrey follows and interrupts the meeting. Garth too is a fully trained Alpha but one thing lets him down - his howl, and that is how wolves find their mate, when their howls match. Humphrey is told to go. Garth begins to howl, and Kate is mortified at how bad he is. Kate escapes the date for a drink of water and runs into Humphrey by the river. They are shortly shot by a ranger, knocked out from the tranquilizer and taken to Idaho.
The two wolves wake up at Sawtooth National Recreation Area and meet a French-Canadian goose named Marcel (Larry Miller) who has an avid interest in golf and his caddy, a duck named Paddy (also voiced by Eric Price). Kate and Humphrey learn that they were relocated to repopulate the species, which upsets Kate. Marcel and Paddy agree to help the wolves return home to Jasper and they hitch a ride in in a camper truck driven by a couple that vacation to Jasper yearly while Marcel and Paddy follow from above.
Trouble brews back at Jasper as the two packs discover that Kate has gone missing. Tony warns Winston that on the next full moon if Kate doesn’t return to marry Garth, he and his pack will declare a war for their territory. Lilly (Christina Ricci), an omega wolf and Kate’s shy younger sister happens to fall in love with Garth and suggests that she wants to show him around. Winston allows that but Tony feels suspicious.
That night when the camper stops by a truck-stop, Humphrey exits the camper to urinate, however he finds a cupcake and eats it. A car has pulled in front of where Humphrey is so Kate cannot see him, and gets worried. A man mistakes Humphrey for a rabid wolf (having creamy covering around his mouth and mistaking it for foam) and prepares to shoot him, but Kate saves him, sacrificing their ride to Jasper which takes off.
That night, Kate finds a ravine and attempts to cross it. She slips down the cliff, but Humphrey saves her by swinging on a vine and telling her to grab his tail. This works, and the two go off to make a den for the night, despite the fact that at first Kate tried to abandon Humphrey out of anger (she may have reconsidered since Humphrey saved her).
The next morning, Marcel and Paddy find the wolves and direct them to a train over a snowy mountain that will take them to Jasper. Climbing the mountain Humphrey meets a bear cub who is unfamiliar with wolves. When they are playing, the cub gets hurt when a snowball is thrown at him and is nearly about to cry, This angers a trio of bears (most likely the cub's parents) who think that Humphrey was trying to harm the cub. When Kate realizes that Humphrey is in danger, she rushes in to help him, causing them to slide down the other side of the mountain on a log (which happens to be one of Humphrey's hobbies). Humphrey saves Kate, and, as the train passes by, the two wolves manage to get into a boxcar just in time.
On the train that night, Humphrey starts to howl at the full moon and asks Kate to join him. She does, after hearing his voice, and the two howl a romantic duet and Kate realizes that this is who she belongs with. Meanwhile at the Howling Rock in Jasper, Lilly helps Garth improve his howl, for which he succeeds and the two howl together. Tony and his pack show up at the scene to prepare to attack the other pack and berates his son for howling with an omega. Lilly retreats to alert her father. Since Kate has yet to return, Tony commands his pack to "take the valley."
Shortly, the train passes by Jasper and Kate and Humphrey return just as the packs begin to fight. Humphrey wanted to tell Kate about his feelings for her, but couldn't. Kate announces that she will marry Garth for the good of the packs, much to Humphrey and Lilly’s surprise and disappointment.
The next day, a heartbroken Humphrey decides to leave Jasper and travel on his own and shares his goodbyes with Kate (which involves him placing a flower in her fur and a playful wink) and Marcel and Paddy who have arrived and decided to stay. Yet Kate feels heartbroken too after learning of how she feels about Humphrey. Halfway through the marriage ceremony of Kate and Garth, however, at the final step, which is rubbing noses, Kate refuses after realizing Humphrey is who she wants to be with. Garth as well declares the same for Lilly. Winston is confused, but Tony and his pack start to fight the other pack out of anger, but the conflict is cut short when a massive stampede of caribou interrupts the scene. Winston and Tony are trapped in the stampede and Kate, including Humphrey who has decided to return both jump in to the rescue. Kate is knocked out when attempting to reach cover, and Humphrey rushes forward to protect her.
After the stampede fades, Humphrey declares his love for Kate, sad because he thinks he never got to tell her. The other wolves including Humphrey and Tony think that she had been trampled to death,all howl as a requiem for Kate. She shortly wakes up much to everyone's relief. Winston and Tony, after having noticed that Kate and Humphrey are in love after they both confess to each other, agree to unite the packs under a marriage between Garth and Lilly, and demolish the rule over social class. The film concludes at the Howling Rock, with all the wolves howling and dancing, including Lilly and Garth. Kate and Humphrey howl a duet at the summit, and the film then ends.