Taking place six months after the first film, Dory suddenly recalls her childhood memories. Remembering something about "the jewel of Monterey, California", accompanied by Nemo and Marlin, she sets out to find her family. She arrives at the Monterey Marine Life Institute, where she meets Bailey, a white beluga whale; Destiny, a whale shark; and Hank the octopus, who becomes her guide.
In the Pride Lands of Africa, a lion rules over the animals as king. The birth of King Mufasa and Queen Sarabi's son Simba creates envy and resentment in Mufasa's younger brother, Scar, who knows his nephew now replaces him as heir to the throne. After Simba has grown into a young cub, Mufasa gives him a tour of the Pride Lands, teaching him the responsibilities of being a king and the circle of life. Later that day, Scar tricks Simba and his best friend Nala into exploring a forbidden elephant graveyard, despite the protests of Mufasa's hornbill majordomo Zazu. At the graveyard, three spotted hyenas named Shenzi, Banzai and Ed attack the cubs before Mufasa, alerted by Zazu, rescues them and forgives Simba for his actions. That night, the hyenas, who are allied with Scar, plot with him to kill Mufasa and Simba.
Two ocellaris clownfish, Marlin and his wife Coral, admire their new home in the Great Barrier Reef and their clutch of eggs when a barracuda attacks, knocking Marlin unconscious. He wakes up to find that Coral and all but one of the eggs have disappeared. Marlin names this last egg Nemo, a name that Coral liked.
Many days after bidding the penguins goodbye, Alex has a nightmare about himself and his friends still being stranded in Africa and finding that they have all gotten old. He then wakes up from his nightmare on his birthday and the animals present him with a miniature model of New York City made out of mud. Alex suggests to his friends and the lemurs that they should go to Monte Carlo to get the penguins and the chimpanzees and fly back to New York City, which they agree to do.
As a cub, Alex the Lion was called Alakay and was the son of Zuba, the alpha lion. Though Zuba tries to teach Alakay to be a hunter, the cub is more interested in dancing, and is captured by poachers when Makunga, Zuba's rival, challenges Zuba to a fight for the position of alpha lion. Alakay is forced into a crate, and taken away despite Zuba's attempts to rescue him. The crate falls into the ocean where it drifts to New York. There, Alakay is renamed Alex and sent to the Central Park Zoo where he grew up, meeting Marty the Zebra, Melman the Giraffe, and Gloria the Hippopotamus. Most of the events of the first film are then described through a series of news flashes.
At the Central Park Zoo, Marty the zebra is celebrating his tenth birthday, but longs to see the rest of the world from outside his pampered life at the zoo, believing that he can find wide-open spaces to run around in, like in Connecticut. Marty's best friend, Alex the lion, attempts to cheer up his friend by singing Frank Sinatra's "New York, New York" with him. Still unsatisfied, Marty gets some tips from the zoo's penguins: Skipper, Kowalski, Rico, and Private. The penguins are similarly trying to escape the zoo. Marty's friends — Alex the lion, Melman the giraffe, and Gloria the hippopotamus — realize Marty's folly and try to follow him. The four, along with the penguins and the chimpanzees Mason and his silent friend Phil, eventually find themselves at Grand Central Station, but are quickly sedated by tranquilizer darts when Alex's attempt to communicate with humans is mistaken for aggression. The zoo, under pressure from animal-rights activists, is forced to ship the animals, by sea, to a Kenyan wildlife preserve. During their travels, the penguins escape from their enclosure and take over the ship, intent on taking it to Antarctica. Their antics on the bridge cause the crates containing Alex, Marty, Melman, and Gloria to fall off the boat and wash ashore on Madagascar.
In the 1880s, an English couple and their infant son escape a burning ship, ending up on land near uncharted rainforests off the coast of Africa. The couple craft themselves a treehouse from their ship's wreckage, but are subsequently killed by Sabor, a rogue leopardess. Kala, a female gorilla who recently lost her own child to Sabor, hears the cries of the orphaned human infant and finds him in the ruined treehouse. Though she is attacked by Sabor, Kala and the baby manage to escape. Kala takes the baby back to the gorilla troop to raise as her own, an act of which her mate, Kerchak, disapproves. Kala raises the human child, naming him Tarzan. Though he befriends other gorillas in the troop and other animals, including the young female gorilla Terk and the paranoid male elephant Tantor, Tarzan finds himself unable to keep up with them, so he takes great efforts to improve himself. As a young man, Tarzan is able to kill Sabor with his crude spear and protect the troop, gaining Kerchak's reluctant respect.
Every emperor 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. Norma Jean, a female penguin, falls for Memphis, a male penguin and they become mates. They lay an egg, which is left in Memphis' care, while Norma Jean leaves with the other females to fish. While the males struggle through the harsh winter, Memphis briefly drops the egg. The resulting chick, Mumble, is unable to sing but can tap dance. Nevertheless, he is enamored with Gloria, a female penguin who is regarded as the most talented of her age. One day, Mumble encounters a group of hostile skua, with a leader who is tagged with a yellow band, which he says is from an alien abduction. Mumble narrowly escapes the hungry birds by falling into a crevice.
In Reef City, an underachieving bluestreak cleaner wrasse named Oscar fantasizes about being rich and famous while making his way to work as a tongue scrubber at the local Whale Wash, a job in which he is following in his father's footsteps. Soon after arriving he is called to the office of his boss, a pufferfish named Sykes, to discuss the fact that he owes "five thousand clams" and has to pay it back by the next day. After explaining this to his angelfish best friend Angie, she offers him a chance to pay back the money by pawning a pink pearl that was a gift from her grandmother. Oscar brings the money to the race track to meet Sykes, but becomes distracted by his dreams of grandeur. Upon hearing that the race is rigged, he places it all on a long-shot bet by the name of "Lucky Day". Such a million dollar bet is noticed nearby by a beautiful lionfish named Lola, who flagrantly seduces an excited Oscar, but Oscar is disappointed when she leaves upon learning that he is a whale washer. Sykes is furious that Oscar bet the money but nonetheless agrees to see how the race turns out. Moments before their betted "horse" crosses the finish line, he trips and falls on the line.
Flik, an individualist and would-be inventor, lives in a colony of ants in the middle of a dried creek. They are led by Princess Atta and her mother, the Queen. The colony is oppressed by a gang of marauding grasshoppers, led by Hopper, that arrive every season demanding food from the ants. One day, when the annual offering is accidentally knocked into a stream by Flik's latest invention, a grain-harvesting device, the grasshoppers demand twice as much food as compensation. The ants trick Flik into accepting his plan to recruit "warrior bugs" to fight off the grasshoppers. While Flik actually believes in the plan, the other ants see it as an opportunity to get rid of Flik and save themselves trouble.
During the end of the Cretaceous era, an Iguanodon mother is forced to abandon her nest during a Carnotaurus attack. The one surviving egg journeys through several predicaments, before ending up on lemur island, where Plio names the hatched baby Aladar and raises him. Years later, Aladar and the lemurs take part in a mating season, where Zini goes without a mate. After the season ends, a meteor strikes and destroys the island, leaving Aladar, Plio, Yar, Zini and Suri, as the only survivors when they swim to the mainland. The family mourns for the loss of all lemurs before moving on.
Ted Wiggins is an idealistic 12-year-old boy , who lives in "Thneedville", a walled city that, aside from the human citizens, is completely artificial; everything is made of plastic, metal, or synthetics. Ted has a crush on local environmentalist Audrey, who wants to see a "real tree" more than anything in the world, and decides to find one in order to impress her. His energetic Grammy Norma secretly tells Ted the legend of the Once-ler, who will tell anyone about trees if you brought him fifteen cents, a nail, and a shell of a great-great-great grandfather snail. When Ted leaves Thneedville in search of the Once-ler, he discovers that the outside world is a contaminated, empty wasteland. Once the boy finds him, the Once-ler agrees to tell Ted about the trees on the condition that he listens to the story over multiple visits. Ted agrees, but on his way home, he encounters the mayor of Thneedville, Aloysius O'Hare, who is also the proprietor of a company that sells bottled oxygen to Thneedville residents. O'Hare explains to Ted that because trees produce oxygen free of charge, he considers it a threat to his business whenever he hears people talking about them. After revealing that he has "security camera eyes" all over the city, O'Hare pressures Ted to stay in town. However, Ted continues to sneak out of O'Hare's sight (with his grandmother's encouragement) and learns more of the trees' history.
While scavenging for food, RJ the raccoon enters the cave of Vincent the bear who has a large wagon full of human food taken from a nearby rest stop. RJ accidentally wakes Vincent from his hibernation, and in a race to escape, causes the stash to roll out onto the nearby highway and get run over. To avoid being eaten himself, RJ promises Vincent that he will completely replace the stash within the week.
In the small town of Oakey Oaks, Chicken Little rings the school bell and warns everyone to run for their lives, allowing the whole town into a frenzied panic with much damage ensuing. Eventually, the Head of the Fire Department calms down enough to ask him what's going on and Little explains that a piece of the sky shaped like a stop sign had fallen on his head when he was sitting under the big oak tree in the town square; however, he is unable to find it. His father, Buck Cluck, assumes that this "piece of sky" was just an acorn that had fallen off the tree and had hit him on the head, making Little the laughing stock of the town.
A dust speck is dislodged from its obscure place and sent adrift through the Jungle of Nool. At the same time, Horton the elephant (Jim Carrey), the jungle's eccentric nature teacher, takes a dip in the pool. The dust speck floats past him in the air, and he hears a tiny yelp coming from it. Believing that an entire society of microscopic creatures are living on that speck, he places it atop a clover. Horton finds out the speck harbors the city of Whoville and its inhabitants, the Whos, led by Mayor Ned McDodd (Steve Carell). He has a wife, Sally (Amy Poehler), 96 daughters (whose names all begin with the letter H), and one teenage son named JoJo (Jesse McCartney). Despite being the oldest and next in line for the mayoral position, JoJo doesn't want to be mayor, and because he's so scared of disappointing his father, never speaks. Once Horton begins carrying the speck with him, the city starts experiencing strange phenomena (earthquakes and changes in the weather), and the Mayor finds his attempts to caution Whoville challenged by the Town Council, led by the opportunistic yet condescending Chairman (Dan Fogler).