Zebra Marty (Chris Rock), Lion Alex (Ben Stiller), Hippo Gloria (Jada Pinkett Smith), and Giraffe Melman (David Schwimmer) are residents of the bustling NY central zoo, where Alex shines as the star of the show, igniting a pang of jealousy in Marty. Meanwhile, a group of clever penguins has been discreetly digging a tunnel to escape to their homeland, Antarctica. One of these penguins shares their daring escape plan with Marty, sparking an idea for the zebra.
On the night of his birthday celebration, Marty boldly reveals his desire to break free and venture into the wild by adventuring onto a train at Grand Central Station. His friends, however, find this dream amusing. Later that night, as they notice Marty missing, Alex, Gloria, and Melman embark on a quick subway ride to locate him, causing chaos among the startled commuters. When they arrive at the train station, they find Marty, only to be interrupted by an elderly woman who hilariously assaults Alex with her purse.
Before long, the penguins also find themselves at the station, leading to a frantic situation where the police corner the animals and incapacitate them with tranquilizer darts. Upon waking up, they discover they've been transported in a crate on an ocean freighter, adrift in the ocean. In a twist of fate, the penguins manage to escape and seize control of the ship, setting their sights on Antarctica. However, the ship capsizes, sending Alex, Gloria, Melman, and Marty overboard and washing ashore on the vibrant beaches of Madagascar.
As they wake up on the strange new terrain, Melman concludes they must be in San Diego, unaware of how far they truly are from home. They soon encounter a whimsical group of lemurs who break into the song "Move It." Just as they approach the lively gathering, a menacing group called "the Foosa," resembling hyenas, threatens to devour a little lemur named Mort. It is then that Alex instinctively comes to the rescue, showcasing the survival instinct that lies within.
The lemurs introduce themselves, particularly their King, Julian ([Sacha Baron Cohen]), and his assistant Maurice ([Cedric the Entertainer]). Here, immersed in the wild, Alex and Marty bicker, with Alex blaming Marty for the whole predicament. In a fit of frustration, Marty opts to go solo, setting up a quaint drink bar. But as Alex struggles to find peace in the noise, he decides to confront Marty, leading to an unexpected moment of camaraderie over drinks.
As the sun rises the next day, the quartet joins the lemurs in revelry within their newfound paradise. However, tension arises when Alex's primal instincts start to resurface, causing him to eye Marty and the lemurs as potential prey. Unable to control his appetite, Alex takes a nibble at Marty, sending the group into a frenzy as they flee. Realizing he's transformed into a predatory version of himself, Alex retreats, deeply conflicted about his nature.
Meanwhile, far away in Antarctica, the penguins struggle against the elements, voicing their displeasure with the situation. Back in Madagascar, Alex ventures deeper into the territory of predators while Marty fortifies his bar, hoping to keep visitors at bay.
As the feelings of worry fester among the beachgoers, the arrival of the penguins signals a glimmer of hope for returning home. Despite warnings against approaching Alex, Marty bravely attempts to coax him back to their group. Unfortunately, the Foosa reappear, triggering a harrowing chase that leads Marty back to the safety of Gloria and Melman. Just when it seems the odds are against them, the penguins make a heroic entrance, but they soon realize they are vastly outnumbered.
In an unexpected turn of events, Alex, fueled by an unhinged determination, swoops in, demonstrating his newfound prowess as a predator. He fiercely declares that this land belongs to him, sending the Foosa fleeing in terror. The animals rejoice as the lemurs throw a farewell party for their new friends, and the penguins prepare sushi to keep Alex satiated and prevent him from reverting to his carnivorous instincts.
As the crew sets sail on their journey home, they embrace the chance to create lasting memories, with the penguins finding a moment of relaxation under the sun. One penguin humorously suggests sharing the boat's fuel predicament, leading to the lead penguin's cheeky response: > "Just smile and wave boys, smile and wave."
