Every penguin sings a unique song called a "heartsong" to attract a mate. If the male penguin's heartsong matches the female's song, the two penguins mate. A penguin named Norma Jean (Nicole Kidman) sings the song "Kiss", whereupon a male penguin named Memphis (Hugh Jackman) sings "Heartbreak Hotel". Norma Jean chooses him as her mate. Norma Jean lays an egg, which is left with Memphis while Norma Jean leaves with the other females to fish. While the males struggle through the harsh winter, Memphis accidentally drops the egg, briefly exposing it to the freezing Antarctic temperatures. The resulting chick - the film's protagonist, Mumble (Elizabeth Daily) - has blue eyes, ever-lasting down feathers, and a terrible singing voice. However, Mumble has a talent that no other penguin has ever seen before: tap dancing. One day Mumble wanders into a secluded area, where he is free to dance without any complaints. Mumble is interrupted when Boss Skua and his posse Dino, Frankie, and Vinnie attempt to eat him. Mumble stalls by asking the leader of the pack about a yellow band that is attached to his right ankle. The Boss Skua tells Mumble that he had been abducted by "aliens". Mumble narrowly escapes the hungry birds by falling into a crevice.
Mumble grows into an adult (Elijah Wood), still half-covered in fluffy down. Mumble joins his class graduates on their first trip into the ocean, where they find a large iceberg to rest on. After interrupting the graduates' song, Mumble is forced to leave, and finds a smaller iceberg. A leopard seal chases him off the iceberg. After escaping the leopard seal, he befriends a small group of bachelors which are Adele Penguins who form a club called "the Amigos": the leader Ramon, the brothers Raul and Nestor, and twin brothers Rinaldo and Lombardo. The Amigos quickly embrace Mumble's dance moves and assimilate him into their misfit group. Mumble's joy is cut short when he accidentally starts an avalanche and causes a hidden human excavator to tumble out from a glacier. Driven by curiosity, he sets out to find the "aliens" responsible for the machine. Mumble has a lot of questions, and the group suggests that he ask Lovelace (a Rockhopper or Macaroni Crested Penguin) who answers questions in exchange for stones and is known as the guru. Lovelace has the plastic rings of a six pack entangled around his neck, which he uses to project his guru image. When asked if the rings were from the aliens, Lovelace denies that aliens exists and claims that the plastic rings were bestowed upon him by mystic beings.
In Mumble's old home, it is mating season, and Gloria (Brittany Murphy) is the center of attention. Although she is surrounded by a large horde of suitors, none of their heartsongs interest her. Ramon tries to help Mumble by singing a Spanish version of "My Way". Gloria is not fooled, however, for she knows Mumble cannot sing. She then notices Ramon behind Mumble's back. Gloria becomes angry and turns her back on Mumble. Gloria continues towards the other males visibly distraught. As a last resort, Mumble tries to persuade her to sing along to his tapping rhythm. Because of her affection for him, she complies. As Mumble's beat speeds up, Gloria finds the chorus to her heartsong, and realizes it is "Boogie Wonderland". Overcome with happiness that they can now be mates, the pair begin dancing, along with the other penguins.
Noah the elder sees their lack of fish as punishment from the Great 'Guin for Mumble's dancing. Mumble tries to explain about the mysterious "aliens", and that they are the cause of the scarceness of fish, but only his mother and Gloria believe him. Noah exiles Mumble from the colony. Mumble vows that he will find the real cause of the famine. He and the Amigos return to Lovelace only to find him being choked by the plastic rings. Lovelace confesses that he got stuck in the rings while swimming near the forbidden shores. He reveals that the forbidden shores are located past the land of elephant seals and beyond the blizzard country. Mumble, the Amigos and Lovelace start their journey. Gloria tries to come, but Mumble, fearing for her safety, drives her off by insulting her singing talents. They travel across vast territories till they reach the shore.
Mumble sees a boat and swims after it. He swims far, and is washed up exhausted onshore. He is rescued and kept at Marine World. He tries to communicate with the "aliens", but when his pleas fail, Mumble nearly succumbs to madness after long confinement. When a girl attempts to interact with Mumble by tapping the glass, he starts dancing, and soon a large crowd gathers. He is released back into the wild, with a Tracking system on his back. He leads the humans to his colony. The other penguins are skeptical, but when Gloria notices the device, they realize that the "aliens" exist. Convinced, the penguins, along with the elders, dance with Mumble to get the humans' attention.
A research team arrives and film the penguins dancing. They bring the footage back and a worldwide debate ensues. The governments realize they are overfishing. Antarctic fishing is banned, and the fish population recovers. At this, the Emperor Penguins and the Amigos celebrate. A dancing baby penguin seen at the end is implied to be the child of Mumble and Gloria.
In the end credits, the characters reunite to dance for the final number, "The Song of the Heart."

Mumble (Elijah Wood) and Gloria's (Alecia Moore (P!nk)) son Erik (Ava Acres) is reluctant to try dancing as most of the penguins in Emperor-land do. Erik's first attempt at dancing embarrasses and outcasts him from the rest of the penguins. After Ramon's (Robin Williams) misguided advice that Emperor-Land isn't fit for outcast penguins like themselves, Erik and his two friends Boadicia (Meibh Campbell) and Atticus (Lil P-Nut) follow Ramon back to Adélie-Land. Upon returning, Ramon learns that Adélie-Land has been ruled by a God-like penguin named The Mighty Sven (Hank Azaria). Sven is the last of his kind who survived death by his ability to fly. Erik instantly becomes enamored with Sven, who takes a liking to him as well as there are "many brave warriors named Erik" back in Svenland. Sven and Lovelace (Robin Williams) tell the story of The Mighty Sven, who was rescued by a Russian vessel and rehabilitated alongside Lovelace. One night Sven discovers the "aliens" that saved them cooking and eating chicken meat. He flees the boat with Lovelace in tow. The two wind up on the shore of Antartica, where Sven performs his first miracle by revealing moss to the local penguins. Ramon accuses Sven of being a fraud and a false idol, until Sven uses his power of "Svending" to help Ramon find a mate. Ramon instantly falls in love with Carmen (Sofía Vergara), another Adélie penguin who shows no interest in him. Mumble follows the chicks' footprints to Adélie land and orders them to return to Emperor-Land. The chicks refuse, especially Erik, who has adopted Sven as a hero. Sven encourages Erik to believe in himself, because "Sven believes in you", before sending Erik back to Emperor-land with Mumble.
Meanwhile, the story shifts to two krill in the midst of a swarm. Will (Brad Pitt) is an adventurous and existentialist krill determined to discover what lies beyond the krill swarm. His friend Bill (Matt Damon) reluctantly follows him to ensure his safety. Once separated from the swarm, Will and Bill realize that krill are at the bottom of the food chain, created to be eaten. Inspired, Will ventures out to evolve and "move up the food chain", eating a real creature instead of being eaten.
On the way back from Adélie-Land, Mumble tells Erik that he is unique to the world and that he will someday find his calling. Erik, still inspired by Sven's words of wisdom, quickly dismisses Mumble's advice. While trying to cross a perilous ice bridge, the penguins encounter Bryan the Beach Master (Richard Carter) and his two young sons, who refuse to let the penguins pass. Suddenly the ice gives away and Bryan is trapped in a deep crevice below the ice. Mumble sets out to free Bryan by antagonizing a sleeping leopard seal until it chases him down. In actuality, it is the work of Bill and Will "moving up the food chain" and trying to eat a creature with a face that awakens the seal. During the fight, Mumble manages to use the leopard seal to shatter the wall of ice between Bryan and the sea, saving his life. Seeking acceptance from Erik, Mumble is disheartened to learn Erik attributed the feat of courage to Svending, Sven's motivational process of achieving what one wants by willing it to happen. Bryan returns to the Elephant Seal beach, but not before thanking Mumble and promising to return the favor to him at any time.
When the penguins returns to Emperor-Land they are shocked to discover a large iceberg has struck their home, trapping the entire Emperor Penguin population below large walls of ice. Boadicia ventures out to Adélie Land to recruit the help of Ramon, the Amigos and all the Adélie penguins to bring fish to the doomed Emperor penguins. In the meantime Mumble, Erik and Atticus deliver meager supplies of fish to the trapped penguins. Erik, still convinced penguins can fly through Svending, attempts to deliver a fish to Gloria by flying and nearly tossing himself over the edge of the ice-berg. Mumble scolds Erik for his beliefs, claiming that no penguin can fly and that none of the Emperor Penguins will be able to escape. Once Erik realizes Emperor-Land is destined to die, he begins to break down. Gloria sends Mumble off to hunt for fish, calming Erik and the rest of the hysterical Emperor-Land through song (Bridge of Light). In the process, Bill becomes inspired to create another swarm of krill but Will refuses, preferring to adhere to his new predator lifestyle.
The next morning, a large flock of Skua attack the trapped Emperor-Land. Noah the Elder (Hugo Weaving) encourages the penguins to stand up to the birds (Anthony LaPaglia, Michael Cornacchia) through perseverance and unity. When all hope seems lost, Boadica returns with the entire Adélie-Land, led by Sven, to aid the trapped Emperor Penguins. Sven orchestrates a cooperative effort to feed the trapped Emperor Penguins through hunting and bringing back a flow of fish from the sea.
During this period Will becomes increasingly agitated with Bill's behavior and ventures out alone, into the Adélie feeding swarm, to join "fellow predators". In the process he is whisked away attached to a fish carried by Sven and down into the trapped Emperor-Land.
Suddenly the Adélie penguins recognize the same Russian vessel that saved Sven and Lovelace. Sven, terrified for his life, flees and hides from the humans. Lovelace, meanwhile, swims to the top of an iceberg and dances to attract the ship's attention. He successfully leads the humans back to Emperor-Land, where they begin carving a path up the side of the iceberg to freedom. Halfway through the effort a large storm rolls in, forcing the penguins to huddle up and the humans to flee. The next morning Sven returns, reporting that the ocean has frozen over significantly and there is no chance of the humans returning or the Adélie Penguins transporting food over such a distance. Tensions arise as the Emperor Penguins become frantic at the lack of food and attempt to launch themselves into the air and "fly" out of the crevice. Erik urges Sven to teach the penguins how to fly, but he reveals his true nature. Sven is a not a penguin at all, but a Puffin-- and puffins can fly. He admits that after the loss of Svenland he was lonely and grew to love the penguins who accepted him as a family. Dejected, Sven flies off. Mumble, after watching snow fall into a crevice between chunks of iceberg, begins to tap-dance on the ice and lead the Adélie penguins in a dance to force snow between the ice and weaken it. The plan works well until several chunks break loose, sending a large portion of the Adélies into the doomed crevice. In attempting to save Erik from plummeting over the edge, Mumble injures his foot and is unable to dance and lead the Adélies. Ramon realizes Carmen is trapped below and, risking his own life, jumps off the iceberg to be with her. As he professes his love to her, she immediately falls in love with him.
Sven becomes aware of the dancing and proves himself to be a worthy dancer despite public outcry against him. He leads the remaining Adélies in dance (Dragostea din tei) while Erik and Mumble venture off to the Elephant Seal beach.
Meanwhile Will, weary from the dangers he experienced as a predator on the surface, ventures back into the sea to find Bill, but not before experiencing the penguin's dancing. He is suddenly forced down a crack in the ice and into the sea beneath Emperor-Land. He reunites with Bill and his swarm, who tell him he has the purpose of changing the world and evolving the swarm. Once Bill told the swarm of their position on the food chain and their lives as pure herbivores, they followed him to the safety of the inaccessible ice below Emperor-Land.
Mumble and Erik arrive at Elephant Seal Beach where Bryan is in the middle of a fight of dominance between another large male. Mumble pleads with the elephant seals to help free the Emperor Penguins. Bryan, initially hesitant to return a favor at such a pivotal time of the year, becomes aggressive and threatens Mumble off the beach. Erik, unnerved by the lack of honor and respect from Bryan, discovers his true ability- a strong operatic voice. He sings an impromptu opera commemorating Mumble as his hero for his acts of bravery and chides Bryan for his lack of compassion and gratitude towards him. At the end he runs up and hugs Mumble, accepting him as his inspiration. Touched by Erik's song, the elephant seals travel to Emperor-Land to free the penguins (Rawhide). The penguins and the seals begin slamming the ice on beat, joined by the krill below the ice, to the tune of "Under Pressure". Finally the iceberg crumbles enough for the Emperor Penguins to climb out of the crevice and reunite with their families.