The movie opens with title and credits shown over a submarine traveling under the Arctic Ice. The North Pole has become more than a frozen expanse. It has become a vital highway for world travel and commerce, and not just in the skies. Deep under the ice, atomic submarines traveled until a series of mysterious undersea disasters threatened to close the Arctic route forever. The Sturgeon was destroyed near the North Pole by a mysterious craft. A newspaper headline blares, "Close Arctic Sea Lane After Epic Disaster!"
At the Pentagon, in Washington D.C., a secret meeting was convened at the Bureau of Arctic Defense War Room. Admiral Terhune (Selmer Jackson) introduces the skipper of the atom killer sub, Tiger Shark, Cmdr. Dan Wendover (Dick Foran) to the Secretary of Defense, Justin Murdock (Jack Mulhall), Dr. Clifford Kent (Victor Varconi) and Sir Ian Hunt (Tom Conway). Kent played an important part in the design and development of the Tiger Shark, and Sir Ian was the winner of the Nobel Prize for Oceanography. Terhune itemizes the reports, "Destruction of four surface vessels, Largest, 10,000 tons. Radioactivity in Arctic waters, flow ice and bergs. Peculiar television images preceding each distress call. Seven polar atom subs vanished without a trace." The Tiger Shark is undergoing emergency modifications in the Bremerton Navy Yard. The most unusual modification is a special escape hatch in the keel for the Lungfish--A deep exploration device, sort of an animated diving bell. Terhune briefs Wendover, "The mission of the Tiger Shark is to hunt down and identify the cause of these Arctic disasters. If humanly possible you will remove it."
A very drunk Lt. David Milburn (Paul Dubov) praises his executive officer to Julie (Joi Lansing), who is sprawled on a couch. Dave's wife, Helen Milburn (Jean Moorhead) is trying to make an exit with her husband before he can warn Julie what a wolf the commander can be. Lt. Cmdr. Richard Reef Holloway (Arthur Franz) stuffs a cookie in Dave's mouth before he can do anymore damage to his reputation with the ladies. Helen and Dave are given the bum's rush out the door. Reef is now free to charm the attractive platinum blond. They kiss then have a cigarette. There is a knock at the door and a note shoved under same. Reef opens the orders and is informed his leave has been cancelled.
At the Bremerton Navy Yard, Reef and Milburn meet boarding ship. They exchange hard luck stories of their cancelled leave and board their vessel. Reef is introduced to Kent and Sir Ian. Watkins (Frank Watkins) is ordered by Wendover to escort Kent and Sir Ian to their quarters. CPO Grif Griffin (Bob Steele) is checking in crew. One of the last to report in is Yeoman Chester Tuttle (Sid Melton). The skipper gives Reef one more piece of bad news, he will share quarters with Dr. Neilson. Reef is surprised and disappointed to see it isn't father, but son, Dr. Carl Neilson, Jr. (Brett Halsey). Dr. Neilson's father was supposed to make the trip but had a heart attack. Both are the only two people trained to operate the Lungfish. Neilson and Reef hate each other. The narrator (Pat Michaels) informs us, "The Tiger Shark left her dock at Bremerton at 0335 hours the morning of May 11, on what was to prove the strangest, most fearful voyage ever made by a submarine, atomic or otherwise." Once outside Puget Sound, Wendover would brief the crew.
Grif meets the two frogmen assigned to the Tiger Shark. They are specialists in underwater demolition. The dark haired man is Seaman First Class Powell (Kenneth Becker), and the blond seaman is Carney (Richard Tyler). This is their first trip on a submarine. Wendover shows orders to Reef, then briefs the crew. A week later the Tiger Shark continued north and by May 20 they crossed the Arctic Circle. When Reef and Milburn enter the break room, Neilson leaves. Reef explains to Milburn that Neilson Sr. was an officer that taught engineering and design at the academy, but his son dropped out of school and made anti-war statements. As a result, Capt. Neilson resigned from the Navy, but he was a broken man. Reef goes looking for Dr. Neilson. Tuttle and Powell are dismissed as Reef wants to talk to Dr. Neilson alone. Reef happily announces that father is better and can replace his son on the mission. Neilson informs Reef that he is staying and will complete the mission. A loud bang sends Reef to the con to deal with an emergency. An electrical interference in the water is disturbing the instruments. Wendover orders the sub to submerge, max angle and depth. Sir Ian has a theory. He pulls out a chart of the Arctic and plotted every disturbance and disaster. They form a pattern, "Each incident occurred almost precisely 1,000 statute miles from the Pole. A line drawn through the points of occurrence makes almost a complete circle around the Pole." He also concludes some sort of intelligence is behind it. He also predicts the next point of contact and proposes the Tiger Shark be there and waiting.
They arrive at the spot they predicted and see calving sections of ice coming right for the sub. They dive, but are struck by an ice berg. Some damage has forced a full stop. On their screen they see a saucer shaped object with a bright light on top. It is moving north at a speed of 22 knots. Carney and Powell are sent outside to do a damage assessment. Sir Ian sketches a likeness of the craft and describes it as, "A pure oval shape with the Cyclops-like eye, or turret on top. I'd estimate its' diameter at, oh, 300 feet." He recounts the Homer legend and names the mysterious craft the Cyclops. Kent finds a UFO picture that resembles the craft they found under the ocean. Grif reports damage is minor and they can get underway. The Tiger Shark spent a month traveling to the Pole and back, but did not spot Cyclops. There were more reported disasters. On July 3, Sir Ian and Kent meet with Wendover and speculate that the repeated trips to the Pole might be a power recharging maneuver. They intend to block his way to the Pole and attack. On July 13, they encounter their prey, after sitting on the bottom and waiting. The radiation counter warns them the Cyclops approaches. Their plan is to arm and launch two atomic torpedoes. At a range of seven miles both torpedoes are launched. Cyclops managed to deflect the first torpedo, but the second embeds itself in a jelly-like substance near the hull. Wendover orders the sub to flank speed. He intends to ram Cyclops. The sub rams the space craft and is stopped by the jelly-like substance. But now they are stuck. Full reverse does not pull them free and they sink to the bottom.
Reef proposes they enter the Cyclops and use torches to cut the Tiger Shark loose. Dr. Neilson proposes he take Reef, Milburn and the two frogmen in the Lungfish. They board the Lungfish and head for the Cyclops eye. Dr. Neilson attaches the Lungfish to the eye and they open the hatch. An aperture opens allowing Reef and the other three men to gain access to the interior of the mysterious craft. Reef is the first to notice breathable air under pressure is available, so they won't need their tanks. The interior is very plain, a series of dimly lit walking paths. They spot the bow of the Tiger Shark. The saw teeth of the ram are caught in the break. Reef proposes to cut the teeth away so the Tiger Shark can pull away. Powell is sent back to have Dr. Neilson report to the skipper. Carney begins to cut away the teeth using an acetylene torch. Grif notices that they show movement. The radiation level is rising and they show movement due north at six knots.
Reef hears something strange. He asks Dave if he hears anything, but the answer is no. Dave senses movement, and even Dr. Neilson notices and asks, "I'm getting an impression of movement, Captain. Is that possible?" The Saucer Voice (John Hilliard) calls telepathically to Cmdr. Holloway and warns him not to resist. Dave confirms he did not hear anything. Reef pulls a gun but is told it is useless. Holloway and Milburn head towards the voice. Powell pulls his gun and runs, but he is caught in a force field and fried by what appears to be radiation. He calls to Carney for help. Carney finds what is left of his shipmate smoldering. Carney runs for the exit, but the aperture begins to close. It closes on Carney and crushes him to death. Reef and Milburn approach the lair of the creature. The voice tells Reef to remove his weapon and approach alone. Reef approaches a spherical chamber and peers into an opening. Inside he sees the source of the voice: A tube-like creature with waiving tentacles like the arms of an octopus. It is covered with projections like barnacles. The top of the head has one large eyeball. Reef asks about why he is the only one that can hear the creature. It explains it is a form of thought wave communication. It also explains, "My mission is to study various solar systems and planets. Select the most suitable for colonization." Unfortunately the Earth seems the most suitable. Dave approaches and sees the creature. He fires his service revolver into the creature, but is caught in the radiation beam and cooked. Reef asks why he hasn't been killed and is told, "I want you unharmed, perfect. I have selected you to return with me along with several other specimens for study. We will examine you and the others. Discover desirable features to incorporate in our Earth colonizers." The creature reveals that it is made of living tissue that can heal itself. To stop the creature, Reef fires a flare into the eye of the thing. He runs for the exit. He makes it past the heat rays and closing apertures. Dr. Neilson sees the aperture closing near the Lungfish and holds it open for Reef. Dr. Neilson secures the Lungfish and returns to the Tiger Shark.
The creature repairs its eye while the Lungfish is brought aboard the Tiger Shark. Once aboard Reef reports, "Skipper we didn't kill it. And if that thing ever gets back to where it came from the Earth is doomed and everybody on it." The Tiger Shark pulls back and frees itself from the Cyclops. They watch the Cyclops head for the Pole at a speed of 50 knots. Kent proposes a solution. He tells Wendover, "It's possible I could adapt one of the torpedo guidance systems to the ICBM, so it would home on the saucer when he rises from the Pole." Wendover agrees to the plan. Reef finds a hole in the ice and the ICBM is prepared for firing and they wait. The Cyclops emerges from the ice and takes off. The rocket is fired and homes in on its objective. A direct hit takes out the Cyclops. It crashes to Earth as a fiery lump.
Their mission accomplished, the Tiger Shark returns to the Bremerton Navy Yard. Reef and Dr. Neilson walk out into the night air. Neilson stares into the night sky and ponders which star their visitor came from. Reef speculates, "When this ship doesn't return, they'll decide not to come here after all." Reef is annoyed he lost his little black book aboard the destroyed Cyclops. We close with Reef and Neilson walking away.