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 Central Park Zoo, Samson the Lion tells his son Ryan stories of his adventures in the wild. That night, when the zoo closes, all the animals are free to roam. Samson, Benny, Bridget, Larry, and Nigel were in a turtle curling championship while Ryan was with his friends. Ryan accidentally alerts the Thompson Gazelles which head to the game. Samson and Ryan have a falling-out about the fact that Ryan can't roar and Ryan storms off, even though his father was sorry for what he said. Benny insists that Samson tells the truth to Ryan or he will lose his son. When Samson goes to talk to him, he is not home. Ryan has actually walked into a green box and accidentally gets shipped, which the legend tells will take him to the wild. With the help of a pigeon, Hamir, Samson and Benny go after him, sneaking into a garbage disposal truck with Nigel, Bridget, and Larry coming as well, accidentally throwing Benny off the truck. After passing through Times Square and nearly being crushed in the garbage disposal, the group encounters a pack of rabid stray dogs. Samson leads them through the sewer rather than scaring them off. There, they take directions to the docks from two street wise alligator brothers, Stan and Carmine.
The film is a sub-story to Kirikou and the Sorceress rather than a straight sequel. The movie is set while Kirikou is still a child and Karaba is still a sorceress. Like Princes et princesses and Les Contes de la nuit, it is an anthology film comprising several episodic stories, each of them describing Kirikou's interactions with a different animals. It is however unique among Michel Ocelot's films, not only in that it is co-directed by Bénédicte Galup (who has previously worked with him as an animator) but also for each of the stories being written by a different person (in all other cases, Ocelot has been the sole writer and director of his films).