The movie starts in the past, in an African reserve, when Alekai the Lion was just a little cub, being tutored, by his doting father, Zuba. Alekai is playful & not learning. Zuba shows him his paw, which has an Africa-shaped birthmark on it, which Alekai also has on his paw. Just then, Makunga (Alec Baldwin), a scheming lion who wants to be Alpha Lion, challenges Zuba. Zuba kicks the pride out of Makunga. As the fight is going on, Alekai goes off the reserve and is captured by poachers. Zuba, finds his son missing & goes to rescue, but is shot by the poachers, but he manages to free Aleka's crate which falls in the river. Zuba survives but has a hole in his ear.The crate & Akela reaches New York City (pre-2001) and is fished out and put in the New York City Zoo. Aleka is a hit as he vamps for the people, behind him, a young Marty the Zebra tells a young Gloria (the Hippo) and Melman (the Giraffe) that Alekai's a show-off. Years later, Alekai is now Alex the Lion (Ben Stiller). Marty (Chris Rock) tells Gloria (Jada Pinkett Smith) and Melman (David Schwimmer) his desire to go out in the wild...which, in his mind, means Connecticut. Then, we see a TV news report on the four animals' NY escapade (from the previous movie) and their encounter with the fearsome Nana (Elisa Gabrielli). After they were recaptured, animal rights activists demanded that they be sent back to the wild. During their voyage, their ship went missing, much to the sadness of New Yorkers.In the island of Madagascar, the four animals are now preparing to go back home, thanks to the airplane that the penguins supposedly fixed. King Julien (Sacha Baron Cohen) of the lemurs, dressed as a lady in a cake, and Maurice (Cedric the Entertainer) are coming along. The two monkeys, Mason and Phil, are also there. With the lemurs' help, the plane is catapulted into the air.The plane runs out of fuel and the plane falls out of the sky. As Marty, Alex and Melman scream in terror, King Julien treats it like a roller coaster ride. Their hatch falls open, and he and Maurice are sucked out, with a parachute deploying, causing Julien to yell out, "I can fly!". Alex confesses that he broke Marty's iPod back at the zoo. Marty's brief anger, however, is interrupted when Melman blurts out that he loves Gloria.They crash land & when the dust settles, they look around, wondering where they are. Skipper and the other penguins celebrate their landing, being able to "live with" two unaccounted for (Julien and Maurice). Alex and Skipper initially over the repairs (with Private pulling a switchblade knife at one point).The group encounters a tourist jeep and gets a cell phone that falls out of an old lady's (Nana from the first movie that kicked Alex's butt) bag. Then they go to the edge of a cliff & see animals everywhere - hippos, lions, zebras and giraffes. Melman initially thinks again that they're at the San Diego Zoo (40% sure this time), they quickly realize they're in Africa.They roam around & Alex is reunited with Zuba & his mother. Zuba recognizes Alex from the birthmark on his paw. Matunga is happy as he plans to pit Zuba & Alex against each other & become the alpha lion himself. Marty meets the other zebras (who all sound exactly like him). They welcome him into their fold. Gloria meets the other hippos and becomes the object of attraction for Moto Moto (Will.I.Am), the hippo "hunk". Melman meets the giraffes and asks about medications. They say that now that their witch doctor, Joe, is dead, if any giraffe gets sick, they go into a hole and wait for death. Horrified, Melman volunteers to become the giraffe's witch doctor.Matunga challenges Alex to a rite of passage. Melman, after having helped out a young giraffe with a broken leg, is informed that the brown spot on his neck is a symptom of "witch doctor's disease" and he has 48 hours to live. Meanwhile, the penguins hijack safari jeeps to use to fix the plane, rendering many of the tourists (including Nana, the old lady from the first movie who is a tourist) stranded in the African reserve. The monkeys bring a whole bunch of monkeys as extra help for fixing the plane. Nana leads the tourists to survival. In the rite of passage Alex keeps thinking it is some kind of a dance off, until he is leveled by a punch from his opponent. Matunga asks Zuba to banish Alex. Zuba abdicates as he cant banish Alex & Matunga becomes the Alpha lion.Alex, Melman & Marty are all sad (Marty because all zebras look like him, Melman because he has 2 days to live & that Gloria is having fun with Moto Moto). Julien & Maurice ask Melman to express his love to Gloria & he does, shocking Gloria.The watering hole of the heard dries up & Alex decides to investigate, for which he has to off reserve (& be fair game for hunters). Alex recognizes Marty with the bite mark on his ass from the first movie, pacifies him & asks him to come along. Makunga tells Zuba and Mom that Alex has gone out of the reserve. Zuba runs off immediately in search of his son. At the watering hole, Moto Moto tries to dig for water, but only finds diamonds and gold. Julien and Maurice show up and declare that an animal sacrifice to the volcano will please the water gods. Melman, thinking that he has less than a day to live, volunteers. Gloria protests, trying to talk Melman out of it, but he has made up his mind.Alex and Marty go through the eerie woods and come up to the source of the water blockage - a dam erected by the New York tourists, led by Nana. Alex is caught in a rope trap. He tells Marty to go get help. At the volcano, Melman stands shakily at the edge of the precipice, overlooking the red-hot magma. Suddenly, the old witch doctor, Joe, shows up. He says that all giraffes have brown spots, so there's no such thing as "witch doctor's disease". Gloria runs up to Melman to tell him not to jump but stumbles and grabs him by his horns. They profess their love for each other. Just then, Marty runs in and tells them that Alex is in trouble, and they need the plane.At the crash site, the monkeys are on strike, Mason and Phil are negotiating with Skipper, and demanding maternity leave (even though the monkeys are all males). Gloria, Marty and Melman run up and tell them to get the plane ready immediately, but Skipper can't until he "breaks the union". However, Phil comes up with "incriminating" photos of Skipper and his bobble-head doll. Skipper grants their maternity leave, and the monkeys get right to work.Alex is taken to the tourists' colony, where they plan to roast him for dinner. Just then, Zuba shows up and frees Alex. Seeing that the tourists are New Yorkers, Alex starts doing his famous dance. The tourists recognize Alex, who they thought was dead. Zuba also joins in the fun. However, Nana still wants to eat them and aims the shotgun at them. Suddenly, the plane flies overhead and drops a bucket down, with a monkey-chain (several monkeys holding hands). The lions get inside and, thanks to some miscommunication up the monkey-chain, the penguins are ordered to take out the dam. Nana stands on top of the dam and tries to shoot the plane down. Out of bullets, Nana waves her handbag right before the bucket strikes the dam like a wrecking ball, smashing it and sending the water back down the river.Meanwhile, at the volcano, Julien and Maurice stand alone at the precipice, wondering about the sacrifice. Suddenly, along comes Mort, who survived the fall and the ocean, and is currently trying to survive the huge, scary shark that's followed him inland. As the shark lunges at the lemurs, they hang off the edge of the precipice, while "Jaws" plummets to a fiery death below. At that moment, they see water flowing towards the watering hole, leading them to believe that the sacrifice worked.The parched animals are overjoyed to see the water back. They are happier when they see Alex and Zuba standing proudly on the capsule, floating on the water towards them. Makunga comes along and haughtily tells them that, though they brought the water back, Alex is still banished. Alex tells him that he has a gift for him and gives him Nana's handbag. Makunga takes it happily, but the gift has an accompaniment inside the capsule - Nana! Seeing her handbag around Makunga's shoulder, she screams "Bad kitty!" and attacks him, leading him away by the ear. Zuba picks up the fallen scepter and offers it to Alex. Alex refuses, but Zuba insists they at least share it, both as Alpha Lions, as the animals rejoice.We then see the animals at a wedding. Although initially Gloria and Melman are seen in the center of the wedding party, it eventually pans down to the real couple: Skipper the penguin and his hula dancer bobble-head doll, her head held to the body with duct tape. Melman comments off-hand that the marriage will never last. The penguins and monkeys fly off in the plane for a honeymoon in Monte Carlo, to be paid for with the earlier-found diamonds and gold. Alex, Marty, Melman, Gloria and the lemurs are content to wait in Africa until they return. Alex tells Zuba that they'll be staying with them. Zuba has an angry look on his face but does the "happy face/angry face" gag, with his paw. They all laugh. Melman and Gloria look lovingly at each other, and Melman blubbers about what he loves about her.