The FT Squad travels to New York City, but in a realm similar to the one where Kyle and his teammates came from, but one where they can talk with animals. They reach the Central Park Zoo, where they meet Alex the Lion, Marty the Zebra, Gloria the Hippopotamus and Melman the Giraffe. They become good friends, but they all get shipped out of town after a frantic search for Marty, who was willing to spend an evening outside the zoo. They all end up on the island of Madagascar, where they meet a group of lemurs led by King Julien. They also encounter Speedy the Snail, a friend who the FT Squad met in a previous adventure. But Alex becomes frustrated about this and is going to extreme measures to get rescued. This puts friendships under strain, and this threatens himself and others when his predatory instincts start to arise.
- Rex, Elsa, Dweeb and Woog aren't going to be in this adventure, due to already meeting Alex and his friends in Simba, Timon, and Pumbaa's Adventures of We're Back! A Dinosaur's Story, when they were trying to reach the Central Park Zoo, along with King Julien, Maurice, Mort, Zuba and Florrie.
- Yao, Ling, Chien Po and Colonel Hathi also won't be in this adventure. Kylgrv thought it would be unfitting for Yao, Ling and Chien Po to be shipped in crates like Alex and the others, and Colonel Hathi is a Future Time Travel Authority.
- The story of this adventure will continue in The FT Squad's Adventures in Madagascar: Escape 2 Africa.
- Kyle will reveal that he is associated with Skipper, Kowalski, Rico, and Private, the penguins from the zoo. He is on good terms with them and Skipper considers Kyle an honorary penguin, even though he is an otter.
- Madagascar is Kylgrv's favorite Dreamworks movie.