At the Central Park Zoo, Alex the lion, Marty the zebra, Gloria the hippo and Melman the giraffe prepare for another day of visitors while the Penguins plan their escape ("It’s Showtime"). Zookeeper Zoe, Zookeeper Zeke and Zookeeper Zelda rev up the crowd. Marty, feeling down about being trapped in the zoo, daydreams about what life would be like on the outside ("Wild and Free"). The other animals throw Marty a surprise birthday party, but when he shares his wish to go to the wild, they burst his bubble by telling him that he’s crazy. After the other animals leave, Alex sticks around to cheer up his buddy ("Best Friends"), and talk him out of leaving. Despite the pep talk, Marty escapes from the zoo.

Alex, Gloria and Melman scour the city in search of their friend. Once they are reunited, everyone tries to remain calm, despite the commotion of the city and the threat of capture by Police Officer 1, Police Officer 2 and Animal Control Officers ("Relax, Be Cool, Chill Out"). Tranquilizer shots bring the adventure to an end ("Grand Central"), and the animals fall asleep. When they awaken, the Zoosters, Mason and the Penguins are trapped in crates on a ship bound for Africa. The Penguins take control of the ship and steer wildly, causing the other animals’ crates to fall overboard. Unaware, the Penguins set off for Antarctica ("Penguins’ Sea Shanty").

The Zoosters reunite on land, suspecting that they have been moved to the San Diego Zoo. After saving a lemur from the Foosa — catlike, carnivorous creatures — the gang is welcomed to Madagascar by a herd of Lemurs and the illustrious King Julien the Thirteenth ("Welcome to Me!"), who gets the party started ("I Like to Move It"). As everyone gets acquainted, King Julien hatches a plan to make friends with the newcomers so that the herd will continue to be protected from the Foosa. Seaweed on a stick is the only food that the Lemurs have to offer their guests, but they provide them a comfortable place to sleep. Everyone is content as they drift off to sleep, except for Alex, whose appetite was not satisfied by the seaweed ("Steak").

Meanwhile, the Penguins reach Antarctica ("Sea Shanty – Reprise") but promptly turn around when they realize that it is not the paradise they expected. When Alex, Melman, Gloria and Marty wake the next day, it appears that Marty’s birthday wish has come true ("Living in Paradise"). However, things take a turn when Alex’s natural instincts and hunger begin to surface. Worried that he might hurt his friends, Alex leaves.

The Penguins arrive with the ship, and Marty sneaks away to find Alex in Foosa territory ("Foosa Hungry"). Alex warns Marty to go away, but Marty refuses ("Best Friends – Reprise"). As the Foosa surround Marty, Alex hatches a plan. The others arrive just in time to help scare the Foosa away ("The King of Madagascar"). Everyone celebrates: the Lemurs are safe, the friends are reunited and the Penguins have the ship to take everyone home ("Together Forever"). One last song ("Move It – Reprise"), and the journey to Madagascar is complete!