Professor Williams and Dr. Gabrielle White are working on an archaeological dig at a sacred Indian ground, and he discovers something big. At a press conference at Scholl Museum, it is unveiled as a prehistoric hieroglyph that Williams claims is evidence of a green giant that terrified prehistoric people 30,000 years ago.
There is then a flashback of a Hulk in prehistoric times. He has longer hair than his modern version and wears a skin loincloth instead of pants. There are shots of him scaring prehistoric people and then holding the hieroglyph.
David, who is in the audience, realizes the hieroglyph represents his own transformation, for it seems to depict a smaller person turning into a green giant. He has found evidence that another person, from prehistoric times, had the same condition as his own. And there is something very odd about the hieroglyph that David also notes: while the green giant holds a club in his right hand, the normal man is holding what looks like a branch in his left hand.
Naturally, David is anxious to learn all he can about his prehistoric counterpart and the connection of the branch to hulking-out; could it even be a cure? So, going under the name of "Bolton", he tries to join the dig. He is surprised when Gabrielle takes him on instantly. Later, he finds out that it was because Gabrielle has recognized him as Banner, because he inspired her when he guest-lectured at her university. She wants to know why he is playing dead and why he wants to join the dig. David tells her the truth. He surmises that the prehistoric Hulk was created from some sort of explosion that produced an overdose of gamma radiation, perhaps from a supernova.
David uncovers a cave that looks like a burial chamber with the remains of the prehistoric Hulk. As they emerge with the bones, they are accosted by Little Jim, Frank and Ricky, who are Indians that are concerned about the archaeological dig violating their sacred grounds. They go back to their tribe, where Little Jim's father, Lone Wolf, tells children stories about the prehistoric Hulk; to the tribe, the prehistoric Hulk is sacred. He brings unity between tribes, and the reason he is green is to transcend hatred between races over color. Little Jim & Co are not impressed with such stories, though they agree with Lone Wolf that the spirits are angry over violations of sacred grounds. They tell the children to take action to protect what is theirs against white people, who only take from them. To show they mean business, they go back to the dig and sabotage a beam to cause a gradual cavern collapse.
Meanwhile, Gabrielle has been examining the prehistoric Hulk's remains; the skull is confusing because it seems to be two skulls. David suggests that it is one skull that shows the prehistoric Hulk died mid-metamorphosis, between his two forms.
They go back to the dig, where the Professor is working. He has just uncovered an intriguing plant fossil when the cavern finally collapses, trapping both the Professor and Gabrielle under debris. David cannot shift the debris Gabrielle is caught under. Then more debris falls on him, which triggers a hulk-out right in front of Gabrielle. The Professor does not see the hulk-out, but recovers just in time to see the Hulk go into action.
The Hulk has no trouble shifting the debris to free Gabrielle and the Professor. He then clears the entrance by smashing right through it. Later he helps Lone Wolf and his grandson Michael (Little Jim's son) whose truck has gotten bogged down. To them, this confirms what Lone Wolf was saying earlier about the green spirit who transcends color hatreds.
Gabrielle and the Professor hold another press conference at the museum in the wake of what happened in the cave. The Professor does not know what to make of what he saw and is evasive in his answers, calling what he came across a "missing link". However, rumors about what really happened are already flying. This has brought McGee to the press conference. Gabrielle tries to fend him off, but he guesses the truth. However, others are scorning the Professor as a fraud and his reputation has become clouded.
McGee catches up with Lone Wolf and Michael. They confirm they sighted the Hulk, who to them is a spirit that is angry over the disturbance of his sacred place. Little Jim & Co show up and reiterate their anger over white people's disrespect for Indian ground and property in the name of archaeology. They are also angry with McGee for not showing enough interest in their concerns to do a story about it, and tell him to shove off.
Meanwhile, at the museum Gabrielle and David have been conducting an amino-acid analysis on the remains, which finds radiation damage in the protein remnants. This confirms there was indeed a prehistoric predecessor of the Hulk. They think the plant fossil is the key to a cure and get to work.
McGee comes in, forcing David to hide. Gabrielle again tries to fend McGee off, and when he persists she calls security. McGee still persists, and also grumbles about the Indians, whom he calls "troublemakers". Gabrielle tells him that those "troublemakers" are her people; she grew up on the reservation and her name was Whitecloud then. After McGee is removed, she tells David she felt caught in the middle, between two worlds. For this reason she changed her name from Whitecloud to White. David has some sympathy for the Indians and tells Gabrielle she may have underestimated people's tolerance.
Little Jim & Co become desperate for something that will grab press attention to their position. Poking around in the dig for something to help them, they come across the newspaper report about the hieroglyph at the museum. This prompts them to go and strike at the museum, and Frank is armed with a rifle.
Meanwhile, David and Gabrielle are making headway on the plant. Then the Professor comes in and says the Board of Directors has withdrawn funding because of his loss of credibility. In the morning, all the equipment has to go. David and Gabrielle are now racing against time to identify the plant, and eventually succeed.
Then Little Jim & Co arrive. The museum is closed, but they trick the guard into opening the doors. They knock him out and lock the doors behind them. They meet up with Gabrielle. They recognize her but call her a traitor to her people, and demand the bones be returned. Gabrielle refuses and argues that she is still loyal to her people, but the Indians do not listen. They lock David up while trying to open a cabinet to take the bones. Then the Indians are surprised by the Professor. This causes Frank's gun to go off, and the Professor is hit in the shoulder.
The injured Professor causes an argument among the Indians because Frank wants to use him for blackmail purposes in their cause. David looks on and struggles to get out, but to no avail. But when Frank starts hitting Gabrielle, this triggers a hulk-out. The Hulk smashes free, downs Frank and breaks his gun. The Hulk carries the Professor to safety, smashes the door down, and runs off. The police arrive and arrest the Indians. As Little Jim is taken away he apologizes to Gabrielle; the sight of the Hulk in person has made him reconsider his father's stories.
There is another press conference at the museum. The Professor says he and the others saw something that they cannot yet explain. However, he will return to the dig. He now has new funding, which he will use to set up a museum on the reservation. After he recovers from his injury he will be off on new expeditions.
David phones Gabrielle. She tells him they cannot find a plant that matches the one they have identified in the fossil, so it must be extinct. David is again disappointed in his quest to find a cure, but he tries to put a brave face on it. Gabrielle tells him she is returning to the reservation and changing her name back to Whitecloud.