The movie opens on Marty’s 10th birthday (middle-aged for a zebra). His friends try to give him a great birthday, but somehow, Marty wants more. He escapes the Central Park Zoo, in which he lives, and makes a dash for the wild. His friends, Alex the Lion, Melman the Giraffe and Gloria the Hippopotamus flag him down, but as they're about to take him back to the zoo, police officers appear in all directions, tranquilize the animals, and send them on a ship to Kenya. However, the penguins take over the ship and the four friends are washed up on the shores of Madagascar.
Once on the island, the animals begin to panic except for Marty, who has had his dream fulfilled. Marty sets up a "bar" on the island, known as Casa del Wild (in English Home of the Wild). Alex is mad at Marty for getting them shipped to the wild, but he later apologizes to Marty and actually begins to enjoy himself on the island. Unfortunately, his enjoyment brings on his killer instincts, causing him to attack the resident lemurs and his friends, including Marty. Alex doesn't "go savage" for long, and is later able to rejoin his friends as they head back to the zoo.
Marty, along with his friends has only a few small cameos in The Madagascar Penguins in A Christmas Caper. He, Alex, and Gloria are seen at the beginning decorating Melman's neck with Christmas lights. At the end, he, his friends, and almost all the other zoo animals are seen singing their own version of "Jingle Bells".
Marty is more than happy to help his friends save Christmas and shows his usual enthusiasm throughout the special.
Marty (along with the other animals) finds himself stranded in Africa. There, he joins a herd of zebra that all look and sound exactly like him. While he enjoys this new lifestyle at first, he quickly becomes depressed when it becomes evident that he has no individuality in a herd. Marty also becomes sad when Alex is unable to tell him apart from the other zebras. Ultimately, Alex is able to make amends by picking Marty out of the herd (later revealed to be due to the bite mark left on his backside from the previous film) and Marty accompanies his friend to unblock a dam set by stranded New Yorkers in the jungle (which causes the watering hole to dry up). When Alex is caught, Marty gets the other animals to help rescue him.
Marty meets a female Okapi who strikes his fancy, but she's not that interested... until Marty finds a love potion (thanks to the penguins) and puts it on! Now she is paying him attention, unfortunately, so are 90% of the females on the savannah! At first this is great, but after a while, Marty finds that being irresistible isn't all it's cracked up to be.
When the zoosters decide that the penguins have taken long enough to return back to pick them up, Marty and his friends go to Monte Carlo in order to try and find them. Unfortunately, they find themselves spotted by the humans in the casino as well as finding the penguins. As a result Marty and pals find themselves being chased after by animal control. In order to hide, Marty, Melman, Gloria, and Alex decide to hide with Circus Zaragoza in order to stay away from the animal control. While hiding they find that this particular circus could earn a contract for an American tour with a stop in New York City, when the group finds that this circus is not going to earn that contract without a serious makeover, Marty and pals take it upon themselves to refresh the circus with some new acts. Marty ends up finding his calling in doing a routine with Stefano in which they are shot out of cannons. When the group ends up getting the contract and reaching New York City, Marty and his friends end up realizing that the zoo is not all it is cracked up to be and decide to instead run off with the circus and continue performing in their acts... After telling their new friends they've changed their minds, Marty, Melman and Gloria were happy seeing Alex and Gia together as a couple. Marty sees that he and his friends are finally where they belong, which is truly crack-a-lackin.
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