To find the reason for the water's blockage, and save their lives, Alex decides to be a hero and venture off the reserve. First he stops by the zebras, apologises to Marty, who joins him. Meanwhile Alex's father Zuba (Bernie Mac) is warned by Makunga (Alec Baldwin), and chases after him.
Alex and Marty find a tribe, led by the old grandma, who have made a dam. Suddenly the people turn against the animals, Marty makes a run for it to get help while Alex is captured and tied up ready to be roasted. He is saved by Zuba, but the hungry New Yorkers surround them.
Doing what he does best, Alex performs his zoo-dance act, and the audience love him. His dad even joins in, and is finally proud of his son.
The penguins fly onto the scene, with the help of the monkeys, and airlift the lions away. They also smash the dam with the air-lift carriage type wrecking ball.
Back on the reserve, King Julien is about to sacrifice Melman to the volcano. Gloria talks him out of it - and also the old witch-doctor turns up, so Melman wasn't about to die anyway.
Mort (the best character in it), still chased by the shark, is ecstatic to see the King and the shark dives past them into the lava. Just then the water flows through into the reserve.
Makunga still wants Alex to be banished, but the old lady has hitched a ride and, thinking he has stolen her purse, beats him up and chases him away. Zuba and Alex now share the role of Alpha-lion.
It ends with a wedding - between the lead penguin and the hula doll(!) The penguins use the plane to take a quick honeymoon, using the gold they found earlier to hit the casinos in Monte Carlo, and plan to return later to take the animals back to the zoo. Gloria and Melman are together, and Alex knows he will always recognise Marty due to the bite marks in his butt from the first movie.