The film begins with a raid by the apelike Wagabu tribe on the Neanderthal Ulam tribe, who possess fire in the form of a carefully guarded small flame which they use to start larger bonfires. Obtained from a natural source, it must be fed constantly to keep it alive, for the Ulam do not know how to make their own fire. Driven out of their home after a bloody battle with the Wagabu, the surviving Ulam escape but are chased into a marsh by a pack of wolves. The Ulam fire tender escapes with the tribe's remaining fire, however after crossing a marsh, the moisture and wind douse the embers, leaving the tribe doomed to die from exposure and starvation. The Ulams refuse to resort to cannibalism and the elder decides to send three men, Naoh (Everett McGill), Amoukar (Ron Perlman) and Gaw (Nameer El-Kadi), out on a dangerous quest for fire.
After a frightening encounter with a pair of saber-toothed cats, the Ulam scouting trio enters territory of the Kzamm, a tribe who have resorted to cannibalism, and capture members of the Cro-Magnon Ivaka tribe as victims. When Gaw and Amoukar pretend to be berserker madmen, creating a ruse that causes the Kzamm tribe to scatter, Naoh manages to steal some fire, but not without being injured in a fight with two of them. One of his injuries is a bite to the genitals, and he spends a fair amount of time in visible agony from this. After killing his opponents and disposing of the Kzamm's remaining fire in contempt, Naoh rejoins Gaw and Amoukar.
A young woman named Ika (Rae Dawn Chong), an Ivaka prisoner who escapes with Naoh, follows them in gratitude, seeking protection. Despite attempts by Amoukar to drive her off, she follows, eventually taking advantage of a food-gather by Amoukar and Gaw to approach Naoh. She makes a primitive poultice, helping him recover from his injury. She also performs fellatio on him, as evidenced by the sudden look on his face, to soothe his pain, and perhaps to ingratiate herself with him.
The four begin their trek towards the Ulam, followed by the Kzamm. Attacked by the hostile tribe, the group takes advantage of a wandering herd of Wooly mammoths to make good their escape. While they travel back towards the Ulam grounds, Amoukar attempts to have sex with Ika: she hides near Naoh, who then demonstrates his claim on her by raping her in front of the other two males.
One day, Ika recognizes that she is near her home. She tries to persuade the Ulam trio to go with her, but either the men's sense of purpose or the lack of a common language with the woman (or perhaps both) keeps them together on their way back to the Ulam. However, when Ika leaves them the next morning, Naoh is upset; at first he continues without her, but finds he cannot stop thinking about her. He turns around, followed by the reluctant Gaw and Amoukar. After Naoh leaves the others to scout a village, he is trapped in a marsh, nearly sinking to his death, but is discovered and captured by the Ivaka.
At first, Naoh is teased and subjected to several forms of humiliation by the Ivaka, but eventually they accept him and show him their ways, initiating him into the tribe. The Ivaka is the most advanced tribe depicted. They have atlatls (spear throwers), arts (body painting, huts, ornaments, primitive pottery), and most importantly, the ability to make fire. When Naoh is taught by Ika how to make fire, he is overwhelmed and his life is changed forever.
Growing impatient, Gaw and Amoukar go to find Naoh and are also captured by the Ivaka. During their ordeal, they are disturbed to realize that one of the teasers laughing at them is Naoh, initially unrecognizable as he now wears the full body-paint of the Ivaka. When Gaw and Amoukar begin their escape during the night, Amoukar tries to inform Naoh of their plan but Naoh pretends that he doesn't understand their native language. Frustrated from the day's events, Amoukar 'persuades' Naoh to come along by knocking him unconscious. Ika follows the trio and helps them escape.
On their way back home, the four run into a trio of Ulam hunters, led by Aghoo, Naoh's rival as dominant male of the tribe. Left by Naoh and Amoukar to guard the fire with Ika, Gaw is severely wounded in a fight with a mother cave bear, barely managing to escape. The other three members of the group find Gaw, and Amoukar carries him over his shoulder. When attacked by the Ulam rivals, the group uses several atlatls stolen from the Ivaka to dispatch their enemies. Thus the group demonstrates the advantages of embracing new technologies.
Naoh and Ika make passionate love during a cloudburst, first by the initial, "animal" style short, rough copulation from behind seen several times before, eventually shifting around to the "missionary position", a position the Ivaka attempted to teach Naoh during his initiation. Intrigued and aroused by observing them, Amoukar approaches, Gaw, who immediately rebuffs him. They also begin to finally understand the concept of laughter, something that had puzzled them earlier about Ika and the Ivakas. When Gaw is hit on the head by a small, falling rock, they all (even Gaw) burst out laughing.
Finally rejoining the Ulam tribe, the group present the fire to the delight of all. The fire tender, having been given the flame, prompts the tribesfolk into an outburst of joy. Due to the ensuing euphoria, the fire tender ends up falling in the water, extinguishing the fire. The enraged tribe nearly kills the fire tender, until Naoh, Gaw and Amoukar restrain them and scold the group. Naoh then tries to create a new fire the way he'd been taught, by using some sticks, dung and dry grasses. After several failed attempts, the more experienced Ika takes over, carefully rubbing the dry sticks together. Once the spark is lit, the tribe is overjoyed, cheering and overwhelmed again.
In the end, Naoh discovers that Ika is pregnant with their child. Naoh caresses Ika while they both gaze at the brightly lit moon.