Plot summary

In the middle of the southern Pacific Ocean, a thousand feet below the surface, what is believed to be an alien spacecraft is discovered after a ship laying transoceanic cable has its cable cut and the United States Navy investigates the cause. The thickness of coral growth on the spaceship suggests that it has been there for almost 300 years.A team made up of marine biologist Dr. Beth Halperin (Sharon Stone), mathematician Dr. Harry Adams (Samuel L. Jackson), astrophysicist Dr. Ted Fielding (Liev Schreiber), psychologist Dr. Norman Goodman (Dustin Hoffman), and U.S. Navy Capt. Harold Barnes (Peter Coyote) are tasked with investigating the spaceship. The team (along with two navy technicians) 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 makes several discoveries. The first is that the ship is not alien, and that it is in fact an American spaceship. They assume, due to the years of coral growth and advanced technology, that the craft is from the future. The last date in the ship's log, 06/21/43, does not indicate the specific century.The last entry in the log 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. An item of particular interest is 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 which 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 begins to show up on the habitat's computer screens, and Harry and Ted are able to decipher the messages and converse with what appears to be an alien (which calls itself "Jerry"), which has been trapped in the sphere. They soon discover that "Jerry" can hear everything they are saying aboard the Habitat.Harry's entry into the sphere prevents the team from evacuating before the arrival of a powerful typhoon on the surface, forcing them to stay below for almost a week. A series of tragedies then befalls the crew: Fletcher, the navy technician, is killed by aggressive Sea Nettles. 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 except for Norman. Norman enters the Sphere to hurt Beth later than the others. 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 spelled "Harry"; it is Harry's subconscious communicating with them through their computer system whenever he is asleep.At that point, Beth's suicidal thoughts manifest themselves as triggering 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 film ends with the three deciding to use their powers to erase their own memories before being debriefed, in order to prevent the knowledge about the sphere from falling into the wrong hands. Thus, Harry's paradox, in which they are alive, yet no one has learned about the "unknown event," is resolved. As they erase their own memories of the "unknown event," the sphere is seen emerging from the ocean and flying off into space. (There is an alternate ending which does not feature the special effects of the sphere, first at the bottom of the ocean, and then flying off into space. Instead, it just includes their decision to forget, followed by one or two lines from each character demonstrating that they have forgotten what happened while a helicopter flies off into the distance)