A spacecraft, presumed to be of alien origin, is discovered on the floor of the Pacific Ocean, estimated to have been there for nearly 300 years. A team of experts, including marine biologist Dr. Beth Halperin (Stone), mathematician Dr. Harry Adams (Jackson), astrophysicist Dr. Ted Fielding (Schreiber), psychologist Dr. Norman Goodman (Hoffman), and U.S. Navy Capt. Harold Barnes (Coyote), are assembled and taken to the Habitat, a state-of-the-art underwater living environment located near the spacecraft.
Upon examination of the spacecraft, they are perplexed to learn it's not alien at all, but rather American in origin. However, its technology far surpasses any in the present day. The ship's computer logs cryptically suggest a mission that originated either in the distant past or future, but the team manages to deduce that the long dead crew were tasked with collecting an item of scientific importance. Goodman and Halperin discover the ship's logs, with the last entry noting an "unknown event." A holographic re-enactment of the event reveals that hundreds of years in the future the ship encountered a black hole, which apparently led to the ship crash landing in the ocean, back in the 1700's. Soon after, Goodman and the others eventually stumble upon a large, yet perfect sphere hovering in the cargo bay. They cannot find any way to probe the inside of the sphere, as the fluidic surface seems to be impenetrable. Upon observation, Goodman ominously notes the sphere reflects everything in the room except them.
Once they return to the Habitat Harry hypothesizes that everyone on this team is fated to die. Harry notes that the black hole is referred to as an "unknown event" in the future logs. However, here in the present they have knowledge of the historic event, yet it's unable to be explained later on. During the night, Harry returns to the spacecraft, is able to enter the sphere, and then returns to the Habitat. The next day, the crew discovers a series of numeric-encoded messages appearing on the computer screens; the crew is able to decipher them and comes to believe they are speaking to "Jerry", an alien intelligence from the sphere. They find Jerry is able to see and hear everything that happens on the Habitat.
A powerful typhoon strikes the surface, and the Habitat crew is forced to stay in the Habitat several more days. During that time, a series of tragedies strikes the crew, including attacks from aggressive jellyfish and a giant squid, and equipment failures in the base, which kill Ted and the team's support staff. The survivors, Beth, Harry, and Norman, believe Jerry is responsible. While waiting for rescue, the three realize that the hazards are manifestations of their own fears: all of them have entered the sphere, which has given them the ability to make their imagination real. Norman discovers that they had misinterpreted the initial messages from Jerry, and that the entity speaking to them through the computers is actually Harry himself, transmitted while he is asleep.
Under the stress of the situation, Beth has suicidal thoughts which causes the detonation mechanisms on a store of explosives to engage, threatening to destroy the base and the spacecraft. They race to the Habitat's mini-sub, but their combined fears cause them to re-appear back in the spacecraft. As a psychologist, Norman is able to see through the illusion. He triggers the mini-sub's undocking process and overrides the others' fears that they will not escape the destruction of the Habitat and spacecraft. The sphere is untouched by the explosions.
The mini-sub makes it to the surface as the surface ships return. As Beth, Harry, and Norman begin safe decompression, they realize that they will be debriefed and their newfound powers discovered. They agree to erase their memories of the event using their powers, ensuring the "unknown event" paradox is resolved. The sphere rises from the ocean and then accelerates off into space.
Dustin Hoffman as Dr. Norman Goodman
Sharon Stone as Dr. Elizabeth "Beth" Halperin
Samuel L. Jackson as Dr. Harry Adams
Liev Schreiber as Dr. Ted Fielding
Peter Coyote as Capt. Harold C. Barnes
Queen Latifah as Alice "Teeny" Fletcher
Marga Gómez as Jane Edmunds
Huey Lewis as Helicopter pilot
Bernard Hocke as Seaman
James Pickens, Jr. as OSSA Instructor
Michael Keys Hall as OSSA Official
Ralph Tabakin as OSSA Official
based on the 1987 novel of the same name by Michael Crichton