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แจ๊ค ไรอัน นักวิเคราะห์ของซีไอเอ ต้องเข้ามาเกี่ยวข้องกับเหตุการณ์ตึงเครียดสับสน ในการตามล่าเรือดำน้ำของรัสเซียลำหนึ่งที่กัปตันได้ละทิ้งเรือไป

Red October is a new Soviet Submarine. When the Americans are given photographs of it, they are extremely curious as to why is it so special. Jack Ryan, a CIA analyst, consults with a friend, who deduces that it's equipped with a new engine that can make it run virtually silent and with such a device, they can position themselves on the outskirts of any coastal city and launch their missles and not give their target any warning.

Marko Ramius the sub's captain kills their political officer after they open their orders which basically has them conducting routine maneuvers but he kills him and burns their orders and replaces it. He then tells the crew that they are going to test their new engine by positioning themselves by New York and run missile drills. Ryan is then called by his boss to attend a briefing that concerns Red October.

It is at this briefing that they discover that Ramius sent a letter to high ranking Soviet official, who after reading the letter went to meet with the Soviet Premier and it was shortly after that meeting that the Soviet navy was deployed to find Red October and sink it. Everyone assumes that Ramius has turned rogue but Ryan who once did research on Ramius assumes that he might be trying to defect.

While everyone dismisses him, the National Security Adviser tells Ryan to go out there and find out for sure if he is right cause once Ramius is in position to fire his missiles they have take him out. Ryan reluctantly goes and is not use to fieldwork, is having a hard time coping with the sea. At the same time someone in the Red October crew knows that Ramius has deviated from his assignment and is doing what he can to stop him.