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A thousand feet below the surface of the Pacific Ocean, an alien spacecraft is discovered. The thickness of coral growth on the spaceship suggests it has been there for almost 300 years. A team made up of marine biologist Dr. Beth Halperin, mathematician Dr. Harry Adams, astrophysicist Dr. Ted Fielding, psychologist Dr. Norman Goodman, and U.S. Navy Capt. Harold Barnes investigate. The team (along with two navy technicians, Fletcher and Edmunds) are housed in a state-of-the-art underwater living environment called the Habitat during their stay on the ocean floor. Upon entering the spaceship, the team discovers the ship is American, not alien. They assume, due to the years of coral growth and advanced technology, the craft is from the future. The last date in the ship's log does not indicate the specific century and details an "Unknown (Entry) Event", which depicts the ship apparently falling into a black hole, resulting in its trip through time. The ship's mission apparently involved gathering objects from around the galaxy to bring back to Earth; this includes a large, perfect sphere in the cargo hold. It is suspended a few feet above the ground and has an impenetrable fluid surface which reflects its surroundings but not, for some undetermined reason, people.

Harry concludes from the classification of the event that sent the ship back that the Habitat crew is fated to die: it would not have been an "unknown event" if they had lived to report about it, he reasons. Harry soon sneaks back to the spaceship and finds a way to enter the Sphere. Soon after, a series of numeric-encoded messages show up on the habitat's computer screens, and Harry and Ted decipher the messages and converse with what appears to be an alien intelligence that calls itself "Jerry". They soon discover that "Jerry" can hear everything they say aboard the Habitat. Harry's entry into the Sphere prevents the team from evacuating before the arrival of a powerful typhoon on the surface. A series of tragedies then befalls the crew: Fletcher is killed by aggressive jellyfish. Later, Edmunds' corpse is found drifting near the station, her body completely pulverized by what turns out to be a giant squid, which returns to attack the station. In the chaos that ensues, Barnes is cut in half by a computer-operated door, and Ted is burned to death. Sea snakes attack Norman, though he is not injured. Jerry is suspected to be the cause of these incidents.

Eventually, only Harry, Norman, and Beth remain. At this point, they realize that they have all entered the world of the perfect Sphere. The Sphere has given them the power to manifest their thoughts into reality. As such, all of the disasters that had been plaguing them are the result of manifestations of the worst parts of their own minds. The name "Jerry" turns out to have been erroneously decoded and is actually "Harry"; it is Harry's subconscious communicating with them through their computer system whenever he is asleep. At that point, Beth's suicidal thoughts trigger a countdown to detonate the explosives that were brought along to clear away the coral. They abandon the Habitat for the mini-sub, but their fears manifest an illusion of the spacecraft around them. Norman finally sees through the illusion and punches the mini-sub's emergency surfacing button. The explosives destroy the habitat and the spaceship, but (unknown to them) the Sphere itself remains undamaged. As the explosives detonate and create a huge blast wave below it, the mini-sub rises to the surface, to be quickly retrieved by the returning surface ships, permitting the survivors to begin safe decompression once on board a navy ship.

The three decide to use their power to remove it from themselves and erase their memories before being debriefed, in order to prevent the knowledge about the Sphere from falling into the wrong hands. Therefore, Harry's paradox, in which they are alive yet no one has learned about the "unknown event", is resolved. As they erase their memories, the Sphere emerges from the ocean and flies off into space.