"In Madagascar, a group of talking animals living comfortable lives in the Central Park Zoo are sent to a nature preserve in Kenya under pressure from animal rights activists, which results in them becoming stranded in the wilderness along with dangerous predators and, even worse, annoying dancing lemurs.
On the boat ride to Kenya, the crew of the ship carrying the animals is overrun by a group of sociopathic penguins, who take over the vessel and set sail toward Antarctica. Amid the confusion, the main characters are washed overboard and drift to Madagascar, where they learn important lessons about friendship and being true to their own nature, etc.
But what we want to focus on is the penguins hijacking the boat.
Now, the boat was not piloted by animals (that would have been unrealistic), so taking over meant subduing the humans. The next time we see the penguins (after returning from Antarctica), the humans are nowhere to be found. A penguin quips that the people are "on a slow boat to China."
What Happened to the Ship's Crew In Madagascar?