In the depths of the Southern Pacific Ocean, an astonishing discovery lies a thousand feet below the surface—a supposed alien spacecraft. This phenomenon comes to light after a transoceanic cable laying ship mysteriously loses its cable, prompting an investigation by the United States Navy. The extensive coral growth enveloping the spacecraft suggests it has remained undisturbed for nearly 300 years.
A specialized team is assembled to explore this marvel, including marine biologist Dr. Beth Halperin, mathematician Dr. Harry Adams, astrophysicist Dr. Ted Fielding, psychologist Dr. Norman Goodman, and U.S. Navy Capt. Harold Barnes. They are housed in a cutting-edge underwater facility known as the Habitat during their perilous descent to the ocean floor.
Upon their entrance to the spacecraft, the crew makes a startling realization—they discover that the vessel is not alien but rather an American craft. Given the extensive coral overgrowth and its advanced technology, they conclude it is a ship from the future. The last log entry, dated 06/21/43, raises questions about the century of its origin and details an "Unknown (Entry) Event," suggesting that the ship fell into a black hole, leading to a bizarre journey through time. This mission appears to involve collecting objects across the galaxy for return to Earth, including a captivating, perfectly spherical object residing in the cargo hold. This sphere levitates above the floor, featuring a curious surface that reflects everything except for the crew themselves.
As tension mounts, Harry deduces that their mission's classification foreshadows doom; if they had survived to report it, it wouldn’t be marked as "unknown." A restless Harry ventures back into the sphere, where a barrage of enigmatic numeric messages soon appears on the Habitat's screens. He and Ted decipher these messages to communicate with what seems to be an entity named "Jerry," who is trapped within the sphere. They quickly learn that "Jerry" is aware of their conversations.
Harry’s actions inadvertently prevent the team from evacuating just as a powerful typhoon descends upon the surface, forcing them to remain underwater for nearly a week. Tragedy strikes the crew; navy technician Fletcher meets a grim fate at the hands of aggressive Sea Nettles. Later, the body of Edmunds is discovered, mangled and lifeless, revealing the monstrous threat posed by a giant squid. Amidst the ensuing chaos, Capt. Barnes suffers a horrifying accident with a computer-operated door, and Ted meets a fiery end, while Norman endures an attack by lethal sea snakes but escapes without injury. The crew begins to suspect that Jerry may be the orchestrator behind these horrific events.
Ultimately, only Harry, Norman, and Beth emerge from this white-knuckle experience. They soon realize that all three of them, except for Norman, have become ensnared in the realm of the perfect sphere. This extraordinary sphere has granted them the unsettling ability to convert their subconscious thoughts into reality. The disasters plaguing the team are reflections of their innermost fears. The name “Jerry” is discovered to be a misinterpretation; it is actually Harry's subconscious interacting with the crew through the computer while he sleeps.
As internal turmoil reaches its peak, Beth’s suicidal inclinations trigger a countdown for explosives meant to clear coral, pushing them to flee the Habitat aboard a mini-sub. Their collective anxieties evoke an illusion of the spacecraft surrounding them. Norman, unlike the others, finally breaks through this facade and activates the mini-sub's emergency ascent feature. The explosives detonate, obliterating the Habitat and the spacecraft, although the sphere remains unscathed. As the shockwave from the explosives propels the mini-sub to the ocean’s surface, the survivors are rescued by returning naval vessels, allowing them to decompress safely.
The climax unfolds as the three decide to erase their memories before the debriefing, ensuring that knowledge of the sphere does not leak to malevolent parties. This resolves Harry's paradox—being alive yet undiscovered. As they wipe their memories of the "unknown event," the enigmatic sphere emerges majestically from the ocean and ascends into space. An alternate ending omits this spectacular sequence, showcasing only their decision to forget, followed by brief affirmations from each character that they have indeed expunged the memories while a helicopter vanishes into the horizon.
