A mysterious vessel is found deep in the Pacific Ocean, so the U. S. Navy calls a team of scientists to investigate.
A helicopter takes them to a ship in the middle of the ocean and Navy Captain Barnes informs them that they’ve found a spacecraft. In fact psychologist Norman was asked to join the team because he wrote a paper on Unidentified Life Forms, which the Navy has been using as a guide. The spacecraft is buried under eight yards of coral, which means it’s been there for three hundred years and crashed on Earth in 1709.
They think there may be life inside the ship, so the scientists have been brought to establish contact, learn where the aliens came from, and avoid a possible invasion. Lastly, Barnes mentions that the Navy’s sonar detected a low-level hum, so there’s something running inside the ship. While the team gets ready to go underwater, Norman admits to mathematician Harry his report had been a sham, and Harry agrees to keep the secret.
Then the scientists get in a submarine that takes them to a structure called “the Habitat”, which the Navy built as a base to do the investigation. Once they’re deep enough, the team can see the spacecraft and is amazed by its huge size. A Navy dive team gets a robot ready to open the doors to the spaceship, so the scientists walk from the Habitat to the spaceship.
However when they reach the airlock they can’t open it, so astrophysicist Ted uses a hammer and a chisel to try to force it. The trick doesn’t work but leaves a chip on the door, which Harry finds weird because the ship wasn’t even scratched by the crash yet simple tools could damage it. At that moment, marine biologist Beth notices heat emanating from the door, so Barnes makes everyone go back only to watch the door open by itself.
They go inside and Beth notices footprints on the ground, meaning someone has already been there. The team splits to cover more ground and in private, Norman tells Beth about his false report too, admitting he took ideas from sci-fi writers. The duo steps on a platform that moves on its own and takes them to the next floor, where Beth screams because she sees a body on a chair.
It appears to be human and it died from blunt force trauma, it’s also holding a snack called “Smokehouse Almonds”. They conclude they must be on an American ship. Then Beth checks the computer and is surprised to find the records in English.
The flight logs have dates with the year 43 and an item called “Unknown Entry Event”. Selecting it causes a hologram to appear around them, showing a spaceship entering a black hole. Afterward the duo tells the others what they’ve found, and in return Barnes shows them the cargo hold, where they find a huge sphere.
Since it could be a trap, Barnes decides to put up a security camera there. Norman notices that everyone is looking at the sphere yet nobody appears on its reflective surface. The group returns to the Habitat and discuss theories.
Ted thinks the ship didn’t crash, it just got caught in the black hole and traveled through time. At that moment they’re informed that there’s a storm on the surface so they must go back soon. Later in their quarters, Harry tells Norman that he predicts they’ll all die, explaining that the ship entering the black hole is listed as “unknown” on the log because they couldn’t make the report in the first place.
Before falling asleep, Harry says he wishes he could get inside the sphere. Moments later an alarm goes off and Barnes checks the cameras to discover Harry approaching the sphere. His reflection suddenly becomes visible and just like that, Harry disappears.
Barnes announces that they won’t go back to the surface until they retrieve Harry, so Norman puts on a diving suit and returns to the spacecraft. He stares at the sphere and Harry suddenly shows up on the ground. His vitals are normal but he won’t wake up.
When Norman looks up again, his reflection appears on the sphere right before the power goes out and Barnes can’t see them anymore. In a few seconds the power comes back and Barnes realizes that they’re running on internal power, meaning the submarine is gone and they’ll be staying down there for a while. While Norman takes an unconscious Harry back to the Habitat, maintenance worker Fletcher goes out to reset the timer in the mini-sub.
Barnes explains they must do that every twelve hours to let the Navy know they’re still alive. If they forget, the mini-sub will automatically return to the surface. On her way back, Fletcher notices a bunch of jellyfish swimming nearby.
At first it looks beautiful, but soon the jellyfish come closer and begin sticking to her suit. Suddenly she feels the jellyfish inside her body and tries to move away, but the jellyfish chase after her. The damage caused to the suit causes water to get in and Fletcher sadly drowns.
The team brings the body back inside and Norman shares that he was attacked by jellyfish when he was young, so he's been afraid of them since then. Beth takes a closer look and discovers she’s never seen this kind of jellyfish before. Sometime later Barnes talks to Norman in private to scold him for not telling him about Beth’s mental health history, it seems he just learned she once tried to self-delete.
Barnes thinks she may put the mission in danger and an argument ensues, only to be interrupted by Ted telling them Harry is awake. The team gathers in the kitchen and watches Harry eat with much enthusiasm, commenting on the great taste of very simple foods. He also confirms he went inside the sphere but doesn’t say how he did it, which is strange because the sphere doesn’t have an opening.
Then Harry takes another bite of food but when he learns it’s calamari, he starts panicking. Ted does the Heimlich maneuver on him, however Harry clarifies he isn’t choking, he just hates calamari. Moments later Barnes calls Ted to the computer because he’s noticed some issues.
As they try to solve the problem, Harry comes too and points at the numbers on the screen, telling Ted to check if it’s binary code and to decrypt it following the keyboard in a circle shape to match the sphere. Ted does so and the group is shocked to see the numbers are messages sent by someone named Jerry. This mysterious Jerry says simple things like “hello” and “I’m happy”, but Norman worries about what may happen if this entity gets angry.
Later Norman hears a weird thumping sound outside the ship so he contacts another maintenance worker to ask about it but gets no response. Norman informs Barnes of this, and when Barnes checks he discovers the worker is outside the Habitat. Norman and Beth go looking for her, only to discover she’s dead and the noise had been her foot banging on the wall.
Beth takes a closer look and is shocked to notice the body has been pulverized. As Norman and Beth bring the body to the station, eggs suddenly start to fall to the ground. Barnes notices something on the sonar and tells the duo to hurry because the unknown entity is coming closer.
As soon as they make it back inside, the entity disappears from the sonar. Afterward Barnes and Norman go to the computer and discuss a game plan to communicate with Jerry, but at that moment a message appears asking what a game plan is. This means Jerry can hear everything they say.
When Jerry stops sending messages, the entity reappears in the sonar and eggs begin falling outside the Habitat again. Beth points out they should protect the sensor grid, so Barnes tries to activate the high-voltage current but a fire breaks out instead. Soon the entity comes close enough for the team to see it’s a giant squid that starts banging on the Habitat.
The noise doesn’t bother Harry, who continues to sleep in his room. Barnes realizes the pressure is dropping, so he sends Ted to fix it. However when Ted turns the valve, he’s suddenly hit by some electricity that slams him into the wall and knocks him out.
While Norman comes to turn the valve, the squid continues to attack, so Barnes orders Norman to activate the high-voltage current again. As soon as he pulls the lever, the squid disappears, but a fire also starts in the room. While the group rushes to put it out and Ted wakes up to help, the emergency doors get activated, so Barnes jams them with a box to avoid getting trapped.
Unfortunately when he tries to move, the box slips and the door crushes Barnes to death. At the same time a part of the ceiling falls on Ted and gets him stuck, so he tells Norman to get out while the flames take him and kill him before they extinguish themselves. Afterward Norman tries to contact Jerry to ask who put out the flames, but in return Jerry asks if he liked the squid and reveals he can manifest more.
Norman tries to explain how these manifestations are killing people, but the messages just ask him to stop calling him Jerry. Then Norman goes to check on Harry, who is reading “20,000 Leagues Under the Sea”. When Norman mentions the attack, Harry says he slept through it, then he mentions he loves this book but he can’t get past page eighty-seven because it’s too scary.
Norman tells him about all the deaths and the fact most of their oxygen is gone, but Harry remains oddly calm. Later Beth reminds Norman that they must reset the mini-sub. Norman admits to her he’s suspicious of Harry and even thinks he may be responsible for the incidents, so he’ll do the resetting and Beth will keep an eye on Harry to keep him away from the mini-sub.
Then Norman goes out and quickly does the reset, but on his way back, he notices bubbles coming out of his suit and calls Beth for help. However it’s Harry who replies, explaining that he has a faulty valve but he should be fine. Norman keeps moving and when he reaches the ladder, a snake suddenly attacks him.
There’s a lot of struggle and then the creature just leaves, so Norman can return safely to the Habitat. Sometime later, the guys notice Beth going into the spacecraft and ask her why. Beth explains she’s looking for food because they ran out, but Harry says there’s a lot of food in the kitchen.
Norman gets angry and yells at Beth for not keeping watch as promised, he also tells her about the food in the kitchen. Beth checks the fridge and cupboard and gets confused, swearing that she saw them empty earlier. Norman continues to scold her, so Beth snaps and calls Norman out for believing Harry over her and reminds him Norman never told them what he did inside the sphere.
When Norman asks her if she also entered the sphere, Beth just leaves the room. Afterward Norman picks up Harry’s book from the ground, but when he looks up he sees Harry still reading the same book. Panicking, he opens the cupboards and finds more copies of the book, realizing Beth had been right.
Norman goes to the computer and asks Jerry what’s inside the sphere, but the response again asks him to stop calling him Jerry. Desperate for answers, Norman reviews the code and realizes Ted mixed some letters in his decoding: it turns out the entity’s name is actually Harry. Meanwhile Beth leaves the Habitat and sets up some explosives.
When she comes back, Norman tells her that the entity is Harry, who is manifesting the strange creatures around them. He also asks her to read page 87 of the book, which talks about a monster with incredibly long tentacles. The rest of the book is empty.
Since Harry hates squid, he was afraid to keep reading the book, and after going to the sphere he has the power to manifest those thoughts. The duo agrees they need to put Harry into a deep sleep to stop the manifestations, so they search the ship’s medical supplies to find a sedative. Then they sneak into the room and Norman jumps on Harry to hold him down while Beth gives him the injection, causing Harry to fall unconscious.
Later a message arrives from the surface informing them the weather is better so they can return to the surface in six hours. Norman goes to a flooded bathroom to brush his teeth and a snake in the water uses the chance to go up his pants. When Norman screams, Beth rushes to the bathroom and grabs the creature, recognizing it as the most poisonous snake in the world which shouldn't be underwater.
Afterward Beth tells Norman to meet her at the lab, but when he arrives, she locks him inside. She explains he’s the one manifesting the snakes, so she wants him to get a sedative injection too. Norman doesn’t believe it, so Beth keeps mentioning examples: Harry is asleep so the snake couldn’t come from him, and the jellyfish are Norman’s fear just like the squid had been Harry’s.
Since Norman refuses to cooperate, Beth decides to take the oxygen from the room and the lab starts flooding. Still stubborn, Norman dives in to get a canister of oxygen and then escapes through a hatch. While Norman swims outside the Habitat, Beth checks the computer and finds the videos of Barnes questioning her mental health and Norman’s scolding, so she gets anxious and leaves the room.
When Norman comes back he hears her crying and tries to comfort her as he concludes they both were inside the sphere just like Harry. Speaking of Harry, he wakes up and demands an explanation. Norman explains the sphere has given them the power to manifest their thoughts into reality and the same must’ve happened to the original crew, who probably killed each other in their paranoia.
At that moment the computer announces the explosives outside the Habitat have been activated, so they have thirteen minutes to evacuate. Beth explains that those explosives were originally brought to blow up the coral, but she set them up as a defense against the creatures. At first she thinks a new manifestation activated it, but then she realizes her own thoughts did it because she had been considering self-deleting again.
To make matters worse, Harry points out that the explosive will disintegrate everything because the spacecraft has liquid hydrogen. The team immediately rushes to the mini-sub but once inside, they can’t turn it on. Suddenly they’re transported into the spacecraft, so the group starts searching for an exit but only manages to run in circles.
Eventually they end up in front of the sphere, and Norman’s reflection tells him to push the button. Realizing what’s happening, Norman tells his friends to let go of their thoughts, and the group instantly appears in the mini-sub again. Norman pushes the button and the mini-sub finally starts moving towards the surface, getting away just in time to avoid the explosion that completely destroys the Habitat.
Once the mini-sub reaches the surface, the group goes through decompression and finds a private spot to talk. They can’t tell the Navy the truth because they won’t believe them, and the sphere was probably destroyed by the explosion. Beth points out they still have the power, but she’s afraid of manifesting dangerous things or the power falling into the wrong hands.
When Norman says it already is in the wrong hands, Harry gets an idea: they should use the power to make them forget everything they discovered. This would explain how the incident on the ship’s log is marked as “unknown”. The trio holds hands and thinks about forgetting everything related to the mission and their power.
At that moment the sphere comes out of the ocean and flies into the sky at great speed, returning to outer space. When the scientists open their eyes, they don’t understand why they’re holding hands.
