The opening title is against a waterspout and the credits over a kelp forest and other underwater scenes. Narration tells us, "This is operation experiment, a secret base far north of the Arctic Circle. Experiment was the code name for this top priority scientific expedition." Two radar operators (Alvin Greenman) and Charlie (James Best) spot the plane on radar and reports its location. Prof. Tom Nesbitt (Paul Christian/Hubschmid) and the military liaison officer Col. Jack Evans (Kenneth Tobey) observe the explosion of a Hydrogen Bomb. Charlie calls Col. Evans to report a very large object spotted on radar, but by the time Evans arrives it's gone. They chalk it up to something being tossed in front of the radar antenna.
Nesbitt and Evans are reviewing their test results. George Ritchie (Ross Elliott) states, "You know, every time one of these things go off, I feel as if were helping to write the first chapter of a new Genesis." They depart to collect radiation results from forward observation posts. Ice blocks their path by tractor, so they go on foot the final distance. At Post 16 they take a radiation reading and decide it's too high. They decide they should split up; one visit Post 17 and the other Post 18 to limit their radiation exposure. They agree to meet back at Post 16. The weather gets worse. Ritchie spots a large dinosaur and hears its roar. He shouts out to his colleague, but Tom Nesbitt can't hear him. He explores a little further and distracted by the beast falls into a crevice, breaking his leg in the process. Nesbitt completes his task and returns to Post 16 and waits. Ritchie shoots a gun into the air, hoping its loud report will bring help. Nesbitt hears it and responds. Following his tracks left in the snow he finds his colleague. He tries to move him alone, but decides he needs more help. Ritchie tries to warn Nesbitt about "a prehistoric monster." Nesbitt attributes his rambling to the cold, pain, and shock. Then Nesbitt hears and sees Ritchie's "hallucination" himself. The creature's proximity and weight creates an avalanche that buries Ritchie and nearly kills Nesbitt. Nesbitt is brought back to base, barely alive from shock and exposure. The doctor tells Col. Evans to get him to a hospital in the states immediately. Nesbitt comes to and begins to ramble about Ritchie and a monster. He is flown to New York's Hartley Hospital. After a two week physical recovery he is started on "Psychiatric Interrogation for Traumatic Hallucinations." He is introduced to Dr. Ingersoll (King Donovan) who tells him that shock and trauma are the reason behind his dinosaur sighting. Col. Evans arrives to tell him that they found no trace of Ritchie or the beast. His primary care physician, Dr. Morton (Frank Ferguson) insists he rest.
The fishing ketch, Fortune, is out in a storm in the North Atlantic. The captain enters the wheelhouse, his first mate Jacob Bowman (Jack Pennick) is at the wheel. Bowman spots something outside and calls for the Captain, abandoning the wheel as he recoils in fear. They hear a roar and see a huge black shape rise up from the ocean. It destroys their vessel and sinks it off the Grand Banks.
The next morning Nesbitt is having his breakfast in his hospital room and spots the story in the newspaper. Bowman was the lone survivor of the disaster. Nesbitt dresses and visits the Paleontology Department of a local University. He talks to the department dean, Prof. Thurgood Elson (Cecil Kellaway) and his assistant Miss Lee Hunter (Paula Raymond). Elson is sympathetic but does not believe his story. Nesbitt asks if it is possible that the H-Bomb thawed the 100 million year old ice and freed the dinosaur. Elson does not think it possible a creature frozen for that length of time could survive. Lee Hunter interrupts to mention that a herd of Mastadon were thawed in Siberia after thousands of years, "yet their fur intact and the meat still edible." Nesbitt leaves dejected. Dr. Morton examines Nesbitt and tells him he can leave the hospital anytime. The radio is playing in his room and a broadcaster announces a second sea serpent sighting, this time from Marquette, Canada. Capt. George LeMay's ship was destroyed.
Nesbitt returns to work at the Atomic Energy Commission, New York Regional Office. His secretary, Miss Ryan, is glad to have him back. She tells him that Lee Hunter is waiting to see him. She brings the newspaper with the LeMay story and tells him it is worth investigating. She's gathered sketches of the known species of dinosaurs and tells him if he can identify the creature that would be proof. That evening they meet at her apartment to look at the sketches. He narrows in on a few likely candidates, and she helps him identify the one he picks as the Rhedosaurus. She tells him if Capt. LeMay can identify the same sketch that would be proof. He calls Canada to talk to the Captain. LeMay (Leo Mostovoy) answers but can only speak French. Nesbitt asks him about the serpent, and the captain promptly hangs up the phone. The operator tells Nesbitt that he won't talk to him further. Nesbitt makes a personal visit but misses him. He speaks to the newspaper editor. He decides to visit Jacob Bowman in the hospital. He convinces Bowman to return to New York and identify the creature.
Elson is packing for a vacation; Lee is helping him. He notes that Lee is developing a budding romance with Nesbitt. Nesbitt arrives with Bowman in tow. Bowman reviews the sketches and picks the same creature--the Rhedosaurus. Elson is now convinced, and speaks to Col. Evans on the phone. Evans tells Elson he will check with a friend in the Coast Guard if anything unusual is reported.
A lighthouse on the coast of Maine contains a keeper and his assistant. One plays a concertina while the other wipes down the equipment. The creature comes ashore and climbs up the lighthouse, drawn to the beacon. They see it and try to escape down the spiral staircase, but the creature destroys it before they can safely exit.
Col. Evans pays a visit to Capt. Philip Jackson (Donald Woods) at his U.S. Coast Guard office. He tells him the story Nesbitt and Elson told him. He asks about any unusual occurrences. That evening at the ballet, Nesbitt and Lee are on a date when Nesbitt is handed a message. They quickly depart and meet with Elson and Evans at Jacksons USCG office. Jackson explains that in addition to the lighthouse, there was shore wreckage in Massachusetts reported. Elson looks at the chart and sees a pattern. It is following the Arctic Current southward. He concludes the beast is heading for New York, its ancestral home. Elson wants to see it before he can formulate a plan to capture the creature alive. He makes arrangements with Jackson for the use of a diving bell.
On the ship Elson boards a diving bell for their first drop into the Hudson submarine canyon system. Elson is in communication with Nesbitt on the surface and provides periodic reports of progress. He spots the Rhedosaurus, only the shoulder and the leg, but confirms it is enormous. Then as he describes it to Lee Hunter in more detail, it attacks and chews off the bell from the cable. The newspaper story the next day confirms Elson's death.
Longshoremen are working at a New York port facility when the Rhedosaurus comes ashore. What starts as a few people scattering turns into a mob in full panic. People stuck in buildings look on in horror at the panic in the streets and the beast's destruction of property. People abandon their cars on the street and run. A patrolman shoots it with his service revolver, with little effect other than annoying the beast. As he reloads the dinosaur bends down and latches on to him by the head. He lifts him up and swallows him whole to the shock and horror of a woman witness. As it walks the streets of New York it destroys cars, utility poles and buildings. The police respond with greater numbers and rifles. Many people seek refuge in the subway system. The National Guard is called out and the Wall Street and Lower Manhattan area is turned into a battlefield. A newspaper headline indicates 180 dead and 1500 injured during the first rampage. A bazooka team fires a couple of rounds wounding the beast in the neck. The ER doctor (Michael Fox) has concluded that the beast has some very dangerous virus or bacteria in its blood that is fatal to humans. A patrol of soldiers begins collapsing after exposure to large patches of the creature's blood.
Evans and Nesbitt discuss how to eliminate the beast. Anything that will spread the blood particles is out. Just as they think the creature may be dying of its wound, it is announced that the beast is alive and ashore at Manhattan Beach at the amusement area. Nesbitt suggests a radioactive isotope shot directly into the wound.
The Army arrives at the amusement park. The Rhedosaurus is at the Roller Coaster. They wait for the isotope to be delivered. Evans selects his best marksman, Corp. Stone (Lee Van Cleef) for the job. He and Nesbitt don radiation suits and take a roller coaster car to the top for a better shot. Nesbitt retrieves the isotope from a lead lined container and Stone fires it into the beast's neck wound. He scores a direct hit and the beast, now in great pain, damages some of the wooden framework and rails. The coaster they were riding gets away from them, crashes, and starts a fire. The two men climb down the burning coaster while the beast goes through its death throes. The Rhedosaurus knocks out a section of burning coaster framework and makes its way to the beach and collapses. We close with Nesbitt and Lee embracing, then turning to view the dead dinosaur.