Skipper, Kowalski, Rico and Private join forces with undercover organization The North Wind to stop the villainous Dr. Octavius Brine from destroying the world as we know it.

Animal pals Alex, Marty, Melman, and Gloria are still trying to make it back to New York's Central Park Zoo. They are forced to take a detour to Europe to find the penguins and chimps who broke the bank at a Monte Carlo casino. When French animal-control officer Capitaine Chantel DuBois picks up their scent, Alex and company are forced to hide out in a traveling circus.

Four animal friends get a taste of the wild life when they break out of captivity at the Central Park Zoo and wash ashore on the island of Madagascar.