Ice Station's plot follows the events that occur in the wake of the disappearance of a diving team at a remote Antarctic research station. A team of Force Reconnaissance Marines led by Lieutenant Shane Schofield is dispatched to secure the station, where they learn the scientists at the base had discovered something made of metal buried within layers of ice hundreds of millions of years old. As Schofield's Marines set about securing the station, they must deal with French paratroopers posing as researchers, traitors within the unit looking to make sure only certain people know of the discovery, a team of British SAS operatives sent to the station, and a resident within the research team who has already killed one of her co-workers.
What is believed to have been an alien space craft is revealed to have been a prototype of a stealth bomber constructed by the losing tenderer in the bid to construct the original stealth project. Using a plutonium core, the plane is able to render itself invisible to the natural eye at a distance by artificially bending light around itself. The plane is destroyed by Schofield himself after a British warhead removes any trace of the ice station and the events that unfolded there, while evidence comes to light of a conspiracy within the United States government.