Plot
In Kenya, the alpha lion Zuba tries to teach his young son Alakay how to fight, but Alakay is more interested in dancing. Rival lion Makunga challenges Zuba for the title of alpha, but during their fight, Alakay is captured by poachers and put in a crate. Zuba gives chase and breaks the safety harness off of the crate containing Alakay, but is shot in the ear and incapacitated. The crate falls into the ocean and drifts to New York City, where Alakay is renamed Alex, grows up at the Central Park Zoo, and meets his lifelong best friends: Marty, Melman, and Gloria.
In the present day, following their adventure in Madagascar, the zoo animals prepare to return to New York aboard a battered airplane piloted by the penguins, accompanied by King Julien, Maurice and Mort. The plane runs out of fuel and crash lands in continental Africa. The animals find themselves at a watering hole on a nature reserve, and are excited to meet others of their species. Alex is reunited with his parents and impresses them with tales of his status as "the king of New York". Marty fits in with a herd of other zebras who look and sound just like him. Melman, a hypochondriac, is distressed that the reserve has no doctors, so the other giraffes appoint him as their witch doctor. Seeking romance, Gloria attracts the attention of the smooth-talking hippo Moto Moto. Meanwhile, the penguins, Skipper, Kowalski, Rico and Private, set about repairing the plane, assisted by numerous chimpanzees recruited by Mason and Phil. They steal vehicles from humans on a safari and strip them for parts. Nana, a tough old woman who attacked Alex in Grand Central Terminal, takes charge of the stranded tourists and helps them survive in the wilderness for the time being.
The zoo animals' initial excitement however soon turns to disappointment. In a scheme to oust Zuba as alpha lion, Makunga insists that Alex complete a rite of passage which the latter mistakes for a talent contest. It is actually a fighting contest, and Makunga tricks him into choosing Teetsi, the strongest lion as his opponent, resulting in Alex's humiliating defeat. Despondent, Zuba relinquishes his title as alpha to Makunga, who banishes Alex from the watering hole. Meanwhile, Marty is dejected by the realization that the other zebras can do everything he can, believing himself to be no longer unique. Melman comes to believe that he is deathly ill and, having secretly loved Gloria for a long time, is saddened by her interest in Moto Moto. The four friends get into a heated argument with one another due to their predicaments. Gloria has a date with Moto Moto, but loses interest when she realizes he is only attracted to her because of her size. After a pep talk from Julien, Melman finally reveals his feelings for Gloria.
The next day, the animals panic when the watering hole dries up. Determined to redeem himself, Alex mends his friendship with Marty and they leave the reserve to investigate upriver. Julien suggests that offering a sacrifice to the nearby volcano will restore the water. Melman, forlorn and believing he is dying, volunteers to be sacrificed. Gloria stops him from jumping into the volcano, and realizes that he loves her for more than her appearance. Alex and Marty discover that the stranded humans have built a camp and dammed up the river, and Alex is captured by them. Zuba rushes to his aid, but Alex saves them both by dancing for the humans, who remember him fondly from the zoo. Marty, Melman, Gloria, the penguins, and the chimpanzees arrive in the repaired airplane and help Alex and Zuba destroy the dam, restoring the water. Nana is seemingly washed away and trapped under a barrel when Alex and Zuba destroy the dam by crashing into the dam like a wrecking ball using a barrel attached to the penguins' "Super Plane" aircraft, successfully restoring the water to the reserve after she tries to stop them by swinging her handbag like a baseball bat to attack them and defend the dam. Nana is seemingly killed and swept away by the flood, but she actually survives the downstream unharmed, simply remaining stuck beneath the barrel unhurt when the dam was destroyed. Makunga angrily makes a stand for control, but Alex tricks him into being subdued by Nana, forcing him out of power. Zuba offers Alex the title of alpha lion, but he declines, believing the title belongs to his father. Zuba claims the title belongs to them both, and father and son become co-leaders.
Skipper marries a bobblehead doll he salvaged from the plane, and he, the other penguins, and the chimpanzees head off to a honeymoon in Monte Carlo. As for the quartet and the lemurs, they happily decide to stay on the reserve for a while.
