It's the year 2029 and Captain Leo Davidson (MARK WAHLBERG) is stationed on the Oberon, a large U.S. Air Force space station that contains a large collection of apes used for space exploration. When one of his chimps mysteriously disappears in an odd outer space electrical storm, Leo disobeys orders and sets out on a rescue mission. While doing so, however, he's sucked into the storm and transported far into the future where he crash-lands onto a planet teeming with talking apes that rule over subservient humans.
He doesn't have long to think about that, however, as he soon finds himself on the run with other resident humans, such as Karubi (KRIS KRISTOFFERSON) and his adult daughter, Daena (ESTELLA WARREN). They're all quickly captured by the militant apes and subsequently delivered to Limbo (PAUL GIAMATTI), an opportunistic orangutan who specializes in the human slave trade.
As Leo tries to figure out this world, he gains an important ally in Ari (HELENA BONHAM CARTER), a compassionate chimpanzee who believes in human rights and gets away with that unpopular notion due to being the daughter of Sandar (DAVID WARNER), an influential simian senator.
Her beliefs don't sit well, however, with Thade (TIM ROTH), the aggressive chimp who runs the military with an iron fist and the aide of Attar (MICHAEL CLARKE DUNCAN), his right-hand gorilla. Thade wants to eradicate all humans from the planet, and thus it's not long before Ari and former gorilla general Krull (CARY-HIROYUKI TAGAWA) help Leo, Daena and other humans escape.
From that point on, and as he attempts to locate what he believes to be a rescue crew, Leo sets out across the desolate Forbidden Zone, all while trying to elude Thade and his forces, eventually leading to the discovery of answers explaining this topsy-turvy world.