While he might not quite be the king of the jungle anymore, New York City Zoo lion Sampson (voice of KIEFER SUTHERLAND) often regales his adolescent son Ryan (voice of GREG CIPES) with tales of his time in the wild, including handling dangerous wildebeests with his mighty roar. It's frustrating for Ryan, however, since his signature sound is more akin to that of a housecat, and it doesn't help that most of the other animals and even young human kids laugh at his attempts to sound mighty.
Having heard about the "green boxes" just outside the zoo and believing those cargo crates to be a means of escape, Ryan sneaks out of the zoo and curls up in one. But then, the doors are closed and the cart is trucked away, with the cub's pleas for help drawing the concerned attention of Sampson. Although he can't get out right away to rescue his son, the lion plots his course of action that he knows will lead him to the torch-carrying lady wearing a crown of thorns (the Statue of Liberty).
Accordingly, he sets out on his rescue mission, initially unaware that his friends have come along for the ride. There's Benny (voice of JIM BELUSHI), Sampson's best friend, a squirrel who's in love with Bridget (voice of JANEANE GAROFALO) the giraffe who wants nothing to do with him. Larry (voice of RICHARD KIND) the somewhat dimwitted snake is also there, as is Nigel (voice of EDDIE IZZARD), a koala bear who overestimates his speed and other abilities, perhaps due to hating having inspired a line of stuffed zoo toys fashioned in his likeness.
After a brief adventure through Manhattan, the unlikely group of zoo animals commandeers a boat and takes off after the cargo ship containing Ryan. When they crash onto the shores of Africa, they figure all is well since Sampson is from there.
They begin to wonder, however, when his natural instincts fail to kick in, whether regarding eating prey or dealing with a herd of wildebeests led by Kazar (voice of WILLIAM SHATNER) who's decided they should get off the bottom of the food chain by becoming carnivores. As the antelopes set out to find, capture and eat some lions to prove their change, Sampson and his friends try to locate and rescue Ryan before it's too late.