Dr. Norman Goodman (Dustin Hoffman) is called to a location in the Pacific Ocean, for what he thinks is a plane crash. His specialty is psychiatry and dealing with crash survivors. The helicopter pilot (Huey Lewis - yes THAT Huey Lewis!) tells him they've been ferrying all kinds of scientists to this location.Onboard a naval ship, Norman sees astrophysicist Dr. Ted Fielding (Liev Schriber) and biochemist Dr. Beth Halperin (Sharon Stone), but is unable to talk to them. The ship's captain, Harold Barnes (Peter Coyote) briefs them - the plane crash is a spacecraft, a huge ship buried under 300 years of coral. In addition to Beth, Norman and Ted, mathematician Dr. Harry Adams (Samuel L. Jackson) is also on the contact team, which was recommended by Norman many years ago.The team goes through a medical examination, and a dive briefing by an instructor (James Pickens Jr.), who tells them there is "no quick return to the surface". The team takes a sub to the crash site habitat, and they all begin to exhibit signs of nervousness. It's clear that Norman and Beth have some history. The habitat is manned by Edmunds (Marga Gomez) and Alice Fletcher (Queen Latifah), who is directing a Navy dive team to set up a drone by the ship's door.The team puts on dive suits and walks on the seafloor to the spacecraft, and the door opens for them. Beth sees footprints in the dust, and Barnes splits them into 2 groups. Beth and Norman step onto an elevator, which takes them to the bridge. Ted, Harry and Barnes find English text and advanced metallurgy. Beth finds a human skeleton, and deduces the ship is American. The flight recorder shows dates from the future and an entry for "Unknown Entry Event". A holographic display reveals that the ship travelled through a black hole. The team finds a huge sphere in a cargo hold. The sphere doesn't reflect the team members, but everything else.Back in the habitat, Ted theorizes that the ship time-travelled through a black hole and arrived 300 years ago. Harry thinks the sphere is alive, and that since the future ship has no information about the black hole, the contact team will not get a chance to warn anyone; therefore, they are destined to die in the habitat. He also expresses a desire to get into the sphere. At the same time, Barnes gets a message that a cyclone is approaching topside, and the team must return to the surface before it hits.As the team is preparing to return, alarms go off, and video monitors show Harry entering the sphere through his reflection. Due to Harry's disappearance, the return to the surface is cancelled. Norman goes to the sphere, and finds Harry at its base, unconscious. Norman sees his reflection in the sphere, and communications with the surface are suddenly interrupted. Harry is taken back to the sphere, as is Norman.Norman sits gazing out a window, and sees a jellyfish. Fletcher takes some tapes to the mini-sub outside, and is attacked and killed by jellyfish. Beth later analyzes the jellyfish and determines it's not a normal one. Barnes questions Norman about Beth's mental state, and Harry wakes up from his coma, feeling exuberant and making comments about never leaving. He appears calm about Fletcher's death, but freaks out over calamari.Later, as Norman and Ted argue over Ted's jealousy on Harry, Edmunds bring them to the communications center, where the computers are acting strangely. Harry notices the codes on the computer are in binary code. After decryption, the messages reads, "Hello. How are you. I am fine. What is your name? My name is Jerry." Norman worries that Jerry appears to have emotions, and what the repercussions would be if Jerry gets mad.Later, they hear noise outside the habitat, and Norman and Beth investigate, finding Edmunds' mangled body outside. Meanwhile, Harry reads 20,000 Leagues Under the Sea. Norman and Beth bring Edmunds' body back inside, and are attacked by strange egg shapes, with something large approaching.Norman tries to contact Jerry, and discovers Jerry can hear them directly. When Norman asks to talk without Jerry listening, and Jerry becomes petulant, and a large squid approaches the habitat. Jerry says (via computer) "I am here," and the squid attacks. Ted bashes his head while adjusting the internal pressure, and Norman activates the external defense system, which causes a fire. As they rush to combat the fire, Jerry states, "I will kill you all". Ted tries to wake Harry, but can't. Barnes get crushed by an emergency door and Ted is killed by fire, then the fire suddenly is extinguished.After the emergency, Norman talks to Jerry, who exhibits a childlike understanding of life, but immense power. Jerry tells Norman to stop calling him "Jerry". Norman then talks to Harry, who is calm but unaware of the incidents. Norman goes to reset the mini-sub, but on the way back, he gets holes in his suit. Harry watches dispassionately and directs Norman to the airlock, but Norman is attacked by a sea snake.Beth goes into the spaceship, saying she's looking for food. Distrust arises among the 3 survivors, as Beth was supposed to be monitoring Norman during his trek. Norman finds another copy of 20,000 Leagues Under the Sea, and then the entire pantry is full of copies. Beth plants mines around the spaceship.Norman re-calculates the code, and realizes the "j" and "e" are incorrect - they should be "h" and "a", which means Jerry is actually Harry. Later, Norman explains this to Beth and also explains the squid - it's a part of 20,000 Leagues Under the Sea. Norman theorizes the sphere made the change in Harry. Beth and Harry plot to sedate Harry, and he goes under quickly.Beth and Harry get a signal from topside that a sub will arrive in 6 hours. Norman is attacked by sea snakes in the bathroom, but Beth saves him without emotion, saying Norman manifested the snakes. She locks him inside the lab and tells him to sedate himself. When he refuses, she floods the lab, and Norman goes outside the habitat, returning through the main airlock. Meanwhile, Beth begins to doubt her own sanity and Harry wakes up. Norman realizes that all 3 of them went into the sphere, and that is what happened to the original crew.The explosives Beth set become armed. With 13 minutes remaining, the 3 head to the mini-sub. Reality keeps changing, but Norman finds a way to launch the sub. The bombs explode, destroying the spaceship and habitat, but the mini-sub makes it to the surface.Several hours later, the 3 complete decompression, and discuss their story. Norman reminds Harry that they shouldn't be alive, since they made it to the surface, and could tell the authorities what happened. Harry suggests they use their power to forget that they have the power. They count to three, and the sphere rises from the deep and disappears into outer space. Beth, Harry and Norman have successfully forgotten their power...perhaps.