A remote mountain range provides a home for a tribe of hunter-gatherers called the Yagahl, who survive by trapping and killing mammoths, which they call the "Mannak". Here, the young hunter D'Leh has found his heart's desire — the beautiful companion named Evolet, known for her unique blue eyes, whom the Yagahl had found as an orphaned girl, a wise woman of the tribe informs of a future prophecy the girl will bring to the tribe. When the mannak come, D'Leh accidentally wins the "White Spear" which is given to the killer of the mammoth. He also wins Evolet in marriage, but feels he deserves neither, because he won by accident.

When another band of mysterious horse-riding raiders called the "Four Legged Demons" attack the Yaghal camp, they enslave Evolet (along with many others), D'Leh, Tic'Tic and Ka'Ren (D'Leh's childhood rival) pursue the raiders to the end of their known world to save her. Baku is seen sneaking behind them and is soon accepted into the rescue mission. The band of rescuing warriors come in contact with terror birds in the jungle. In this encounter, Tic'Tic gets wounded and later recovers, but Baku and Ka'Ren are captured, with Evolet re-captured . Then, in the desert, they encounter gazelles, Lappet-faced Vultures, and a larger saber toothed cat, similar in appearance to a Smilodon, but larger and more tiger-like in appearance. Along their journey they meet tribes of warriors, who have also had loved ones enslaved by the raiders.

D'Leh and his mentor Tic'Tic befriend Nakudu, leader of the Naku tribe, whose son was taken and wife murdered. Then Nakudu tells D'Leh of their prophecy: that whoever talks to the "Spear-Tooth" (saber-tooth) will help free their people. D'Leh (while hunting for food), had earlier saved a saber-tooth from drowning in a trap which also resulted in D'Leh freeing himself. The saber-tooth then spared his life, and he realizes the prophecy was about him. Nakudu explains that his loved ones were taken in the "Great Red Birds", or ships with large red sails, to the "Mountains of the Gods", from which no one has ever returned. Tic'Tic also takes into account that maybe D'Leh like his father, has a greater destiny than most men. Then they come together with other tribes, who agree to form a coalition and march in pursuit of the captors.

Through the desert tract, they find the ships with red sails holding Evolet and Baku, plus others. They can't follow the ships, so they talk to a desert tribe that advises them to follow the "Eye of the Snake", or perish in the sea of sand. They follow, and ultimately navigate using the moon and North star. At the end of the journey through a vast desert, they discover a relatively advanced civilization similar to ancient Egypt and ruled by an enigmatic figure known as "The Almighty", who is said to be the last survivor of his kind. The Almighty, who is regarded as a living god, possesses many thousands of slaves that he is using to build a huge pyramid complex in his honor and possibly for his burial.

D'Leh and his coalition sneak into the slave quarters, and ask an escaped servant of the Almighty who this Almighty is. D'Leh notices the former servant wears a bracelet that was worn by D'Leh's father. D'leh's father had left his tribe for food, and finding the Naku tribe, taught them his language, before being stolen by the raiders. D'Leh later finds that his father was not a coward, and that he was responsible for saving the servant's life. The servant informs D'Leh that his father's bones are buried in the desert. In a night attack, the guards of the slaves discover the camp of the coalition behind the middle pyramid. Tic'Tic fights three guards, and manages to kill two of them, but the last guard mortally wounds him before he dies.

Meanwhile, the Almighty's priests discover Evolet wears "Uru-Anna" or the "Mark of the Hunter", the brightest star in all heaven, which pertains to the constellation Orion's belt, and after which the pyramids are supposedly modeled. The priests, unaware that her mark was caused by the lashings of the warlord raider, mistake it for part of a prophecy which states that Evolet is somehow destined to kill the Almighty. D'Leh, taking the white spear, rouses the coalition with a great speech. With a plan mapped out, they spark a full-scale rebellion amongst the slaves. The first plan is to cause chaos among the mammoth herd, to cause them to stampede. With the Almighty's troops coming up the slope, Ka'Ren sacrifices himself to give D'Leh more time. The mammoths eventually stampede killing a large contigent of troops.

The Almighty offers Evolet to D'Leh in exchange for him abandoning his rebellion. At last, the Almighty makes a deal with D'Leh, that if he should take his wife, the rest must be his slaves forever. D'Leh feigns the acceptance of the deal which allows him to come close enough to the Almighty to kill him. Once close enough, he throws a spear at the Almighty and kills him, proving him not to be a god. During the ensuing battle, Baku fails to strike the One-Eye man that killed his mother, but when he grabs Tudu the son of Nakudu, Nakudu successfully strikes him with a spear. The warlord raider who had kidnapped Evolet initially, steals her again on horseback. Evolet, slung behind him, reaches into the quiver of arrows that is near her and stabs the warlord in the side. Both he and Evolet fall from the horse. D'Leh rushes towards her when he sees them fall, but the warlord succeeds in shooting her in the back with an arrow. D'Leh reaches her just in time to catch her dying body. He lays her down and runs to have his revenge with the warlord, who tells D'Leh that if he cannot have her, then no one will. D'Leh then kills the warlord with the White Spear as the main temple of the Almighty burns in the background. D'Leh returns to Evolet, and she dies in his arms.

The scene shifts to Old Mother - the wise woman of the Yagahl - as she breathes in deeply and then breathes out her last breath. The scene then returns to D'Leh cradling Evolet's body when she suddenly awakens, fully restored by the wise woman's sacrifice. They depart for home and bid farewell to the other tribes. Time passes and we see that the seeds that D'leh had received during his travels have begun to grow. As he stands, he greets his wife Evolet and they passionately kiss as the screen fades in the sun.

In an alternative ending, the scene then shifts forward many years into the future, showing the old Baku's retelling of the story by the camp fire. It ends with a child asking what had happened to the "Mountains of the Gods", and Baku remarks, "they were taken back by the sands. Lost to time, lost to man".

• Steven Strait as D'Leh (an anagram for "Held" which is the German, Dutch and Afrikaans word for "hero"), a mammoth hunter and the main protagonist.
• Camilla Belle as Evolet, D'Leh's love and the only survivor of a different tribe; one which was killed off by the "Four Legged Demons" (fierce warriors on horseback). While kidnapped, her hands were whipped, leaving a scar in the shape of the "hunter" - a foreshadowing of the one who will defeat the Almighty. She is unique in that she has blue eyes.
• Cliff Curtis as Tic'Tic, D'Leh's mentor.
• Joel Virgel as Nakudu, leader of the Naku tribe.
• Afif Ben Badra as Warlord, leader of the "Four Legged Demons"
• Mo Zinal as Ka'Ren
• Nathanael Baring as Baku
• Mona Hammond as Old Mother, the Yagahl wise old woman.
• Marco Khan as One-Eye, Warlord's main henchman.
• Reece Ritchie as Moha
• Joel Fry as Lu'Kibu
• Kristian Beazley as D'Leh's father, who had lived with the Naku tribe and learned agriculture from them.
• Junior Oliphant as Tudu, Nakudu's son.
• Boubacar Badaine as Quina, leader of another tribe.
• Tim Barlow as the Almighty. The Almighty is a tall, blue eyed man who dresses in long white robes and a face-concealing veil. He also fears the "Hunter", who is foretold to bring about his downfall.
• Omar Sharif as the Narrator / elderly Baku

Production began in spring 2006 in South Africa and Namibia. Location filming also took place in southern New Zealand and Thailand. Before shooting began, the production had spent eighteen months on research and development for the computer generated imagery. Two companies recreated prehistoric animals. To cut time (it was taking sixteen hours to render a single frame) 50% of the CGI models' fur was removed, as "it turned out half the fur looked the same" to the director.