A Savage beast, grown to monstrous size and driven mad by toxic wastes that are poisoning the waters, spreads terror and death on a Maine countryside.
A Doctor (Robert Foxworth) and his wife (Talia Shire), at the request of a concerned friend, travel to Maine to research the impact that the lumber industry has on the environment. They find fish that grow many times their normal size, and also a series of bizarre and grisly murders. Veteran Director John Frankenheimer manages to present "Prophecy" as both a monster movie, and a suspenseful tale about the deadly forces which result from the pollution of the environment.
The idealistic Dr. Robert Verner is invited by his friend Vic to travel to the Maine with his wife Maggie working for the Environmental Protection Agency to prepare a report about the dispute between Indians "Opies" (meaning the original people) and the lumberjacks. Maggie is pregnant but she has not told to Robert since he does not want to have children. Robert and Maggie are welcomed by the director of the paper mill Bethel Isely that drives them to their cabin in the woods. However they find an Indian blockage of the road and witness a conflict between the leader of the Opies John Hawks and Isely and his men. On the next morning, Robert goes fishing and he sees a huge salmon in the river. Then they meet with John Hawk and his wife Ramona and they tell that their people are ill and most of their babies are born with deformation. They also hear about the legendary Katahdin and visit the Garden of Eden of the Opies, where Robert finds weird plants with roots on the surface and a huge tadpole. Robert continues to investigate and discovers that the industry is using methyl mercury in the process that is causing the mutagen in the environment.
A log company's waste mutates the environment, creating a giant killer bear-monster.
- Tracking two lost lumberjacks through the night, a rescue team nearly follows a hound over a cliff. Two men rappel down to retrieve the fallen hound, but they are killed. The third, hearing screams down below, rappels down to investigate, where he finds his team mates dead, only to be killed himself by an unidentified creature.
Dr. Robert Verne is fed up with dealing with the squalor of city tenements. He does not feel he is making a difference. He accepts a job from the United States Environmental Protection Agency to write a report on a logging operation near the Androscoggin River in Maine. The loggers are in a dispute with the local American Indian "Opies" (i.e., "O.P.s"), the original people.
Dr. Verne's wife Maggie accompanies him on the trip. She is pregnant but is apprehensive to tell her husband as he is set against having children. When they fly in, they meet a man, Travis Nelson and his two children Paul and Kathleen who are embarking on a trek into the wilderness. They also meet Bethel Isely , the director of the paper mill, who is to be their host. He tells them about his missing rescue team and lays the blame at the feet of the Opies. The latter have their own explanation: Katahdin, a vengeful spirit of the forest that has been awakened by the activities of the loggers. Isely describes Katahdin as "larger than a dragon with the eyes of a cat".
As Isely drives the couple to their cabin, their path is barred by a party of Opies. They refuse to let Isely's people pass and a fight ensues between the leader of the Opies John Hawks Armand Assante and Kelso (Everett Creach), one of Isely's heavies. The heavy is armed with a chainsaw while Hawks has only a double-bit axe. The scuffle ends with Hawks laid on the ground with the chainsaw nearly at his throat. The Opies relent and let the cars pass. Verne and Maggie are visibly shocked by the incident.
While fishing, Verne sees a huge salmon devour a duck. Later, after he and Maggie have eaten his catch, they are attacked in their cabin by a deranged raccoon. Verne kills it and sends a tissue sample to be tested.
The next day Hawks and his wife Ramona Victoria Racimo approach Dr. Verne to put over their side of the story. If Verne is concerned about the environment then he should include the people in his assessment. Something is making the people ill: still births, mental illness and birth defects are rife. Hawks takes Verne and Maggie to the home of Hector M'Rai, Ramona's grandfather. Hector claims to have seen Katahdin and describes him as "part of everything in God's creation". Verne sees plant roots growing on the surface that should be underground; Hawk nets a bullfrog-sized tadpole from the water to show Verne; Hector has cigarette burns on his hand but feels no pain. As the evidence mounts the idyllic setting gradually takes on a sinister hue.
Verne and Maggie tour the paper mill to look for incriminating evidence but the chemicals used in the processing are demonstrated to never leave the plant. Isely tells them that the water is routinely tested for purity. As they leave, however, Verne notices mercury deposits on Maggie's boots. It is a mutagen that causes birth defects and progressive nerve damage. It has long been used in logging as a fungicide because it is cheap. It will not show up in Isely's water purity tests because it sinks to the bottom. Verne needs more evidence and determines to take blood tests from the Opies.
That night, the Nelson family, who have set up a camp in the woods, are suddenly assaulted by Katahdin; a ferocious bear with one of it's sides containing horribly mutated skin. The horrified Paul tries to flee, but the beast swats him into a rock, killing him. The next day as Verne and Maggie are taking blood samples, Isely and Sheriff Bartholomew Pilgrim arrive to arrest Hawks and his men whom they mistakenly believe to be the ones who killed the Nelson family. Hawks, however, escapes. Verne, Maggie and Ramona take a helicopter to the campsite to investigate the killings. Verne and Ramona find huge scratch marks on the trees while Maggie finds two mutated bear cubs trapped in a salmon poacher's net. One of the cubs is still alive and Verne is determined to save it so it can serve as empirical evidence of the contamination. However, the weather has turned and the pilot, Huntoon, refuses to take off in the high wind.
They make for Hector's home and Verne sends Hawks to fetch Isely and the sheriff. Verne sets up an emergency room in one of Hector's tepees and helps the cub survive. Maggie is clearly distressed by the ordeal so Verne takes her aside and assures her that it will all be over soon. Shockingly, she reveals to him that she is pregnant and she has eaten contaminated fish like the mother of the cubs.
Isely and Sheriff Pilgrim arrive and see the mutant cub. Isely is contrite, knowing that Hawks and his men weren't the killers. Hector arrives, when suddenly Katahdin attacks the camp in search of her cubs and kills everyone in sight. Everyone else seeks shelter in tunnels beneath Hector's home. All goes quiet so Pilgrim decides to check it out. He pokes his head up out of the tunnel and Katahdin kills him.
The next day, the survivors make their way out of the forest. The helicopter is not an option as Huntoon was severely mauled in the beast's initial attack. Isely heads up to Mount Emery to try to reach a radio tower and call for help. Isley finds the radio tower but the monster immediately finds him and before Isley is able to call help, Katahdin kills him as well. The others find the Opie village mysteriously isolated and the Opie people gone, but take a truck and try to drive out along the winding forest road. Katahdin turns the truck over and finishes Huntoon off by devouring his head. The others run off through the forest with the beast in pursuit.
They arrive at the river and swim across. The cub continues to bite Maggie but Rob pulls it off her and holds it underwater, drowning it. Hector stays behind to make Katahdin flee but fails and he is killed as well. Katahdin seems reluctant to follow them at first, but then enters the water and vanishes. They believe she drowned but then she suddenly emerges. They take shelter in a log cabin, but Katahdin tears down the walls. Maggie is knocked unconscious by debris, but Ramona is crushed. It is later revealed that she survived the incident.
Verne finds a Winchester Model 1892 rifle in the cabin and shoots the monster twice with some effect. Hawks shoots arrows into Katahdin's hide until the beast sends him airborne with a mighty swat from her paws, then he lands on the ground, dead and bloodied. Verne picks up an arrow, then Katahdin hoists him up, only to be stabbed repetitively in the face and eyes until she collapses into the lake. Rob notices that the monster still moves slightly and leaps onto the beast and stabs her a few more times until her corpse finally sinks below the water.
Verne and Maggie fly over the forest the next day, but not knowing that there is another mutant animal still alive in the forest.