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The heavy use of the Arctic Circle corridor by the American military comes to a halt when numerous submarines and their crews are mysteriously destroyed. A week after the destruction of the atomic powered submarine Sturgeon , the head of the Bureau of Arctic Defense, Adm. Terhune, summons Cmdr. Dan Wendover to a meeting with scientists Dr. Clifford Kent and Sir Ian Hunt. Terhune informs Dan that his atomic submarine, Tiger Shark , is being refitted with advanced tracking and safety devices to prepare it for a mission to learn the cause of the disasters. Upon receiving orders to cut short his leave, Dan's executive officer, Cmdr. Richard "Reef" Holloway, reports to the Tiger Shark , where he learns to his dismay that he will be bunking with Dr. Carl Neilson. Reef holds a grudge against Carl, who, although a dedicated oceanographer, is also involved with anti-atomic protests. Carl's father, a lifelong Navy officer, instructor, inventor and mentor to Reef, has devoted himself to developing atomic power. Branded a "warmonger" by the press, the senior Neilson was forced to retire from the Navy. When Carl reveals that his father's ill health necessitated his replacement on board the Tiger Shark to test out their jointly developed depth explorer mini-sub, Reef angrily insists that Carl's beliefs have betrayed his father. After the Tiger Shark sets off, Dan waits a few days before revealing the submarine's mission and introducing the officers to Hunt and Kent, who are on board to assist. Several days into their journey, Reef gives a report to Carl stating that his father has recovered sufficiently to join the submarine. When Reef sneeringly suggests this gives Carl the opportunity to evade responsibility, Carl angrily points out that his strong pro-peace politics do not make him a coward and accuses Reef of being a martinet. As Reef declares that he is willing to sacrifice himself for his beliefs and country, the Tiger Shark is abruptly rocked by an explosion. When the amazed scientists state that the ship is being subjected to an unusual electrical storm, Dan orders evasive maneuvers. While descending, Hunt notes a strange light off the submarine's bow. Later, the scientists report to Dan and the officers that all the destroyed submarines had been attacked within an equal radius of the North Pole, a pattern that suggests the assaults were not random. Dan then orders the Tiger Shark to the area where the other submarines were attacked. Upon nearing the Pole several days later, the Tiger Shark is struck by huge blocks of ice. While the submarine undergoes repairs, Hunt draws a picture of what he saw during the electrical storm and the men are startled that the drawing resembles a flying saucer. Hunt describes the unusual glow emitting from an orb on the top of the saucer, which he likens to an eye and dubs "Cyclops." Soon after, the Tiger Shark completes repairs and returns to patrol, and over the next few weeks, more ships and submarines are attacked near the Pole. Hunt and Kent tell Dan that their research of those attacks indicates that Cyclops heads to the Pole after each strike, suggesting that it may require the magnetic field as a power source. Dan decides that after the next attack the Tiger Shark must track Cyclops and place itself directly between it and the Pole. After the destruction of a freighter, the submarine lies in wait for Cyclops near the Pole and soon the saucer appears, giving off low energy levels, thus confirming the scientists' theory. Dan orders two nuclear warheads armed and fired at the saucer, but is startled when the first misses and the other is frozen by a strange substance emitted by the saucer. In desperation, Dan orders the Tiger Shark to ram the saucer. The assault appears to damage the saucer critically, but the submarine is wedged fast to the saucer and the conjoined ships sink to 200 fathoms. Carl recommends using the depth explorer mini-sub to free the Tiger Shark . Accompanied by frogmen Powell and Carney, navigator Dave Milburn and Reef, Carl takes the depth explorer to the saucer, where they land on the orb. Upon entering the barren, darkened saucer, they discover an oxygen atmosphere allowing the men immediately to begin work to free the submarine's bow. On board the Tiger Shark , Chief Griff points out that the radiation levels are rising and the saucer and submarine are actually moving. Hunt and Kent speculate that the saucer is recovering from the blow by the submarine. Meanwhile in the saucer, Reef is startled to hear a voice summoning him, but Dave insists he has heard nothing. Reef pursues the voice toward the interior of the saucer, followed by a concerned Dave. Meanwhile, a strange radioactive light shines on Powell and burns him to death. Fleeing in panic, Carney is crushed in one of the saucer's doors. Unaware of the deaths, Reef reaches a large entranceway and the voice orders him to proceed alone. Entering through a portal, Reef comes across a large creature with tentacles and a huge eye, which communicates through brain waves. The creature tells Reef the ship explores planets to find those suitable for colonization and, having found Earth ideal, intends to return to its home to report. Meanwhile Dave advances and, spotting the creature, shoots it several times, only to be destroyed by a blast of radiation. Reef then shoots the creature directly in the eye and flees back to the depth explorer. While the creature struggles to recover, Reef tells Dan to put the Tiger Shark in reverse. The mini sub returns to the Tiger Shark and they free themselves from the saucer, which immediately flees to the Pole. Kent suggests turning the remaining warhead into a computer-guided missile to fire at the saucer when it leaves Earth. The torpedo is modified and when the recharged saucer blasts out of the ocean, Dan fires it, striking the saucer and destroying it completely. Later, back at their base, Reef and Carl wonder if other ships will come and Carl admits he feels secure knowing the world is protected by men like Reef.