10,000 BC

A remote mountain range provides a home for a tribe of hunter-gatherers called the Yagahl, who survive by trapping and killing mammoths. Here, the young hunter D'Leh has found his heart's desire - the beautiful companion named Evolet. When another band of mysterious horse-riding raiders attack the Yaghal camp and enslave Evolet (along with many others), D'Leh is forced to lead a small group of hunters south to pursue the raiders to the end of their known world to save her. The band of rescuing warriors come in contact with terror birds and a saber-toothed cat in the desert. Along their journey they meet tribes of warriors, who have also had loved ones enslaved by the raiders. Together they form a coalition and march in pursuit of the captors.

At the journey's end through a vast desert, they discover a pre-egyptian civilization ruled by an enigmatic god-like figure known as "The Almighty", who is said to be the last survivor of his kind. It is implied through dialog, and a map in the room of the Almighty, that he is the last of three survivors from Atlantis, and possibly of extraterrestrial origin. The Almighty, who is regarded as a living god, possesses many thousands of slaves who he is using to build huge pyramids in his honor. D'Leh and his coalition attack the slavers, sparking a full-scale rebellion amongst the slaves. However, the Almighty attempts to stop D'Leh by threatening to kill Evolet. D'Leh feigns acceptance of this deal in order to approach the Almighty, killing him with a thrown spear and declaring him not to be a god. During the chaos that erupts around them, the raider who had kidnapped Evolet initially steals her away again on horseback. Evolet, slung behind him, reaches into the quiver of arrows that is near her and stabs the slave lord in the side. Both he and Evolet fall from the horse. D'leh rushes to her side when he sees them fall, but the slave lord succeeds in shooting her in the back with an arrow. She dies in D'Leh's arms. The slave lord tells D'leh that if he cannot have her, then no one will. D'leh kills him in revenge.

The scene shifts to the wise woman of the Yagahl as she breathes in deeply and then breathes out her last breath. Then it 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.