In 2028, the government announces that the world's energy resources will be fully exhausted within five years. To solve this problem, it's been decided to test the Shepard Particle Accelerator in the orbiting Cloverfield Station. If all goes well, this would provide Earth with infinite energy. British engineer Ava doesn't want to leave her husband Michael alone because they recently lost their children to a fire and they should be working on fixing their relationship. But Michael convinces her to join the Shepard mission even if it takes years because they'll all die if she doesn't find a solution. Ava joins a crew formed by American commander Jason, German physicist Ernst, Brazilian doctor Monk, Irish engineer Gordon, Russian engineer Sasha, and Chinese engineer Ling.
The team works wonderfully together but unfortunately they fail at activating Shepard, and they keep trying for the next two years. Ava keeps in touch with Michael through videocalls, and he updates her on the awful state of the world. When Ava needs some extra comfort, she also plays old videos of her children. The mood in the station is tense because they only have power for three more tries and the chances are low. The news they get from Earth isn't encouraging either: the world is coming apart under oil wars and conspiracy theorists believe Shepard is dangerous because it could rip open portals into parallel universes that will bring monsters to Earth. This mood often ends up triggering petty arguments among the crew that end up in actual physical fights that the commander has to stop. The team gets their emotions under control when it's time for the 47th test.
After lots of calculations and care, they finally manage to get a beam going, but it immediately overloads and explodes. The entire station shakes and throws the crew from ceiling to floor, the power goes out, and a fire begins around the Shepard. Ernst puts it by opening the ventilation vents into space, but there's still the matter of fixing the power, which is harder than it looks because for some reason the system is all scrambled. Moments later, they have power again thanks to the backup, because their main power is fried. The O2 tanks are leaking, the reserves are severely diminished, and Ava keeps trying to contact Earth for help to no avail. When the engineers check the comms they make a shocking discovery: Earth is nowhere to be found. The first theory they can think of it's that Shepard has thrown them across the galaxy, prompting Ava to check her own private communicator and sadly confirm she can't contact her husband either. This dire situation triggers another argument among the crew as they look for someone to blame for the malfunction.
Jason takes a moment to cry in private, and once he's calmed down, he breaks up all the arguments and reminds his crew their priority is to survive. Each person is assigned a repair to work on, but when Ava and Sasha go to check on the gyroscope that aids in the station's navigation, they find it missing. That's not the only weird thing happening: Sasha keeps touching his face because he feels something bothering him under the skin, and there are some weird groaning noises coming from one of the walls. Yet another argument begins because half of the crew doesn't want to break a wall and release something dangerous, but they don't have any other choice. As soon as they take the panel off, they are shocked to find a woman named Mina painful stuck among the wires. Nobody knows who she is, but she mentions Ava's name. The crew immediately cuts all the wires and takes Mina out to take her to the infirmary, where they put her to sleep so that Monk can take care of her without more pain.
Meanwhile on Earth, Michael wakes up in the middle of the night when he feels the whole house shaking. Looking through the window shows him lots of explosions outside, and when Michael checks his phone, he sees messages from everyone freaking out over a possible European invasion having reached the USA. Then Michael checks the internet for news, and while the government swears it wasn't a nuclear weapon, they still won't tell what caused the explosions. Michael calls the hospital he works at to see if he's needed, and he gets flabbergasted when he hears the actual facts about what's happening. Back in the station, the crew is arguing again. The gyro is missing, the system is still scrambled, and a mysterious woman appeared inside the wall, so they feel completely lost.
Jason tells everyone to go back to work on the repairs since they're still the priority, but Ernst asks Ling to meet him in the X-deck in ten minutes to see if they can take control of the situation because he's done with Jason's orders. This is overheard by Sasha. While trying to fix Shepard, Ernst snaps and yells at Ling, who quickly puts him in his place and reminds him they're a team. Meanwhile in the rec room, the foosball is moving on its own. In the greenhouse, Gordon discovers the worms are gone. Sasha keeps obsessing with his skin and looking at his face in the mirror, thinking he can see something crawling inside him. Suddenly, his left eye moves on its own, and Sasha begins creepily talking to himself. Then he goes to the 3D printer and makes a gun that he takes to threaten Ernst and Ling, thinking he can make them confess to some secret conspiracy. Sasha starts coughing while he speaks and unexpectedly throws up before falling to the floor as his body goes through a seizure
. Ling puts the gun away while the crew takes Sasha to Monk, but before the doctor can do anything, Sasha throws up the missing worms and dies. A terrified Ava goes to her room to stop herself from having a breakdown, but she returns when she hears Mina has woken up. Jason is wary of this woman, but Ava still approaches her and asks her what she's doing here. Mina wonders the same about Ava and explains she's been in this station for two years, she knows all the others except for Ling. Ava tells her Ling is the Shepard engineer, but Mina says that's her own job and that Ava was supposed to be on Earth. Mina swears Ava had been the team's civilian coordinator and they were friends, but Ava still doesn't know who she is. Upset over the fact nobody knows her, Mina clings to Ava with a hug and whispers in her ear not to trust Ernst because he was the one to sabotage the ship. When Jason learns about this, he checks the system and finds e-mails confirming Ernst is a spy.
Jason immediately goes to find him and beat him up before locking him up in a room as a prisoner, although Ernst swears he doesn't know what they're talking about. In the meantime on Earth, city-wide destruction has been reported. Michael's driving to the hospital while calling people at the base to send a message to his wife, only to hear they've lost contact with the station. Suddenly Michael stops the car because he sees a giant shadow walking away from a destroyed house, where young Molly is yelling for help. Michael takes her with him in the car but they can't go to the hospital because Michael gets a message that the building has been destroyed too. He promises Molly she'll reunite with her parents later, then he takes her to a shelter that belongs to a friend that is out of town where they can wait safely. In the station, Gordon is working on the repairs when suddenly a weird hole appears on the wall and swallows his arm.
This strange hole is capable of moving all over the wall and dragging Gordon with him. Jason and Ava hear him cry for help and come pull him out, but once he's free, Gordon is shocked to discover he's lost his arm. Monk takes a look at it but he can't find any clues, especially since Gordon swears it doesn't even hurt. Things get weirder when the door to Ernst's room opens on its own and he comes out to find something in the corridor that makes him call the crew. Everyone joins Ernst and finds Gordon's arm crawling on the floor. Gordon swears he isn't controlling it, so the crew puts the arm under a glass box while Ernst explains this proves the conspiracy theorist right: the Cloverfield Paradox is real and two realities in a multiverse are fighting to occupy the same space, creating chaos. The arm starts making writing gestures and the crew brings it a pen that the arm uses to give a message: they need to check inside Sasha. They do as the arm says and to everyone's surprise, they find the missing gyroscope inside Sasha's stomach.
They immediately put it back in the system and manage to fix the scrambling, which reveals the station had been upside down and moved during the explosion. As soon as they fix these issues, they manage to find Earth again and while they can't send messages yet, they can receive the planet's signals. The news clips that appear on the screen are weird too: they talk about a fourteen-month-old world war that was caused by the destruction of the Cloverfield station, which fell in the middle of the ocean. Ernst quickly realizes what's going on: there aren't two different realities fighting, the crew and the station jumped into a different universe where the original crew is dead except for Mina. Ernst wants to fix Shepard and fire it again to return home, but Monk and Gordon want to help the people on this Earth. Ling disagrees and thinks it's too late here, so they should go back and prevent this war from happening on their Earth.
Ernst stops the argument by pointing out that going back is their only option because the longer they stay, the weirder effects they'll go through. Later when Monk checks on Mina, she explains her station also failed when Shepard overloaded, and she can tell they are a crew from a parallel dimension. Ernst and Ling think condensation caused the Shepard to overload, so Ling goes to fix the ventilation to help with that problem. Ernst confirms it solves the issue but Ling can't come back because the door has locked on its own and now the room is being filled with water coming out of the ventilation vents. Ernst, Ava, and Jason rush to help her, but they can't override the locking code, and they don't have enough strength to pull it open manually. Eventually the pressure of the water breaks open the outer door, and Ling dies when she's hit by the vacuum of space.
After the crew has a moment to grieve, Ernst wants to get back on the repairs because losing Ling proves being here is dangerous. They can't finish fixing Shepard without Ling though, so Ava points out Mina is the Ling of this universe thus she should have the same knowledge. Jason continues to be wary of her, but they don't have a choice. Back on Earth, Michael's sure the paradox Ava had told him about it's behind all this. He's calling a friend in the force to see if he can locate Molly's parents when suddenly, the shelter begins shaking and a monster roar can be heard outside. In the station, Mina's finally allowed to leave the infirmary, and she accepts to help if she's given all of Ernst's research to help her Earth. Ernst protests, but Jason reminds him they'll leave this dimension and the Ernst from this world is dead, meaning he accepts the deal. Mina will require lots of power to fix the final section of the Shepard, and the guys begin working on that while Ava takes Mina to her new room. Ava also takes the chance to ask why this universe's Ava stayed on Earth, so Mina plays a recording to show her that here her children are alive and she stayed with them. The guys are trying to figure out where to get the power they need to activate the Shepard again and think they could shut down the oxygen temporarily. They would get two hours of oxygen to fire the Shepard, and when they return to their universe, the now working Shepard should provide power to turn on the oxygen again. Ava interrupts them to ask Jason for permission to take a pod to Earth to see her kids. Jason explains this goes against protocol, not to mention Ava may end up seeing herself, but Ava explains she needs to warn her family about the fire that killed them in her world. Jason reluctantly allows her to go. The crew begins working on their plan and Gordon goes to shut down the oxygen tanks.
The idea works and the Shepard begins activating, but Gordon also starts noticing weird magnetic problems around him that take his tools away. The metallic sand he had used to fix the wall also reacts and grabs Gordon, trapping him on the wall before the weird magnetic field causes the oxygen tanks to explode, causing a huge part of the Shepard to blow up. Mina informs the crew that the maintenance deck gets more unstable with every rotation, thus they need to decouple it to survive. While Ava, Jason, and Monk suit up for the mission, Ernst reminds Mina that he isn't the same guy that betrayed her, but she stays cold. The trio goes outside and approaches the maintenance ring, but they find it jammed, which means they'll have to jettison it. Monk and Ava begin making their way back to see if there's a way to do this remotely, but Jason knows it can only be done with the door closed so he stays behind to keep it locked manually.
After saying goodbye to Ava, Jason jettisons the ring, losing his life to save his crew. Meanwhile on Earth, Michael's watching old videos of Ava when he gets a message confirming Molly's parents have been contacted. This inspires Michale to record a video saying goodbye to Ava in case he's dead when she comes back. In the station, Ernst confirms they only have forty-three minutes of oxygen left. Jason left Ava in charge so she gives everyone their next chores, deciding to fire Shepard twice: first to overload it and make it send them back, the second time to make it power the station. She also announces Monk and Ernst can go back, but she'll be leaving with Mina to Earth on a pod. While Monk and Ernst work, Mina takes the chance to steal the gun and takes her to the pod to knock out Ava. Then she activates the pod to make Ava leave alone while Mina goes after the others. Fortunately Ava wakes up quickly and sees this plan, so she must choose between staying in the pod or saving her friends. Mina finds Monk first and shoots him to get the key for the Shepard because she wants to keep it to save her planet. Ava decides to cancel the pod and come looking for Mina, but by the time she arrives, Monk's already dead.
Mina goes after Ernst next, although her shot isn't in a vital spot because she needs him to control the Shepard, although she admits she wants revenge for her crew. Ava arrives and tries to stop her, prompting Mina to point out that Ava can't have both Shepard and her kids, she also swears she doesn't mind killing three people to save eight billion. While the women argue, Ernst picks a tool from the floor and hits Mina, giving Ava the chance to run away. Ernst and Mina fight for the gun, which is accidentally fired and knocks Ernst out. Mina goes after Ava, trying to manipulate her into coming out by playing the recordings of her children. When Mina comes close enough, Ava jumps on her and starts a fight using objects from around the room, allowing her to struggle for the gun and shoot out the window. This causes Mina to be ejected into space while Ava holds herself onto the furniture until she can crawl out of the room and close the door to be safe. Afterward, Ava takes Ernst to the infirmary and takes care of his wounds. Since it's only the two of them left, she can't go back to Earth, so she sends a message to herself to warn her about the fire and remind her that being with the family is the most important thing. Next Ernst and Ava overload the Shepard, and the beam once again transports them between dimensions. The duo can see Earth again and immediately contact the base, confirming Shepard is working and getting permission to come back.
Once the Shepard is activated for a second time to start the production of energy, Ernst and Ava get on a pod to go home. Michael gets a message from the base confirming his wife is fine and soon they'll reunite, but Michael freaks out and asks the higher-ups to tell Ava not to come. As the pod comes closer to Earth, a giant monster bursts from the clouds with a loud roar.