The whole movie is made to look like it was made from a collection of recovered video footage. The movie begins with an introductory screen saying, "The Europa One mission was the first attempt to send men and women into deep space." Various camera feeds are shown of the ship's interior and exterior. In one video, Engineer James Corrigan (Sharlto Copley) is shown recording a video diary; in others team captain William Xu (Daniel Wu) is seen adjusting various panels, Dr. Katya Petrovna (Karolina Wydra) is seen fixing gear, Andrei Blok (Michael Nyqvist) and Dr. Daniel Luxembourg (Christian Camargo) are seen enjoying a floating game of chess and pilot Rosa Dasque (Anamaria Marinca) is seen adjusting panels and monitors in the cockpit. The camera feeds slowly start to get distorted and eventually stop, with the feed from the cockpit of pilot Rosa Dasque being the last image before a static.
Back on what appears to be earth at that present time, Dr. Samantha Unger (Embeth Davidtz) is apparently giving an interview on the Europa One mission, saying, "These were the last few images from the Europa One craft. At that time it had already traveled further than any human being had ever traveled before. For 16 long months I have been asked the simple but loaded question: What happened?..all...I am sorry.." She is visually upset while recalling the mission details.
It appears that somehow the rest of the mission video footage was later recovered and then compiled to tell the story of the crew aboard Europa One.
The footage of Europa One resumes with the team assembled in the central living area, all except James Corrigan. Everyone is upset; it is obvious something bad must have happened. Katya asks about informing 'his' family and whether they should go on. Back on earth Dr. Umber explains she was on board a transatlantic flight when she was informed that feed transmission from Europa One had stopped, and what they expected to be just delayed was already over 15 hours of dead feed.
The recorded video diary of pilot Rosa is shown and she confirms the death of James Corrigan, and how badly it affected the whole team, saying how the "exhilaration of it all left." The rest of the team appear in various camera feeds visibly stressed and broken down, Andrei seemingly most distraught. Daniel and Katya pack James' bag. A year after James' death the team is still depressed and trying to cope.
The mission video feed now goes back 19 months, 10 days and 14 hours to explain the events that lead to the current situation. The viewers are now taken back to the launch day. The administration including Dr. Umber are all excited to introduce the mission and reveal its purpose. The team pull off a successful launch and are up in space on their way to Europa. The 6 man crew, the first to journey beyond the moon, is applauded loudly at mission control. On board James starts his video diary by introducing the ship's interior, their daily life and the rest of the excited crew. Dr. Umber (back on Earth) cuts in saying how far they have come and how far they yet have to go. Several pre-launch interviews are shown explaining that the purpose of the mission is to seek out life in Europa, as it has been confirmed that free water does exist beneath its very thick layer of ice, and even heat signatures have been found in the area called the "Conamara Chaos." On board, the team continues with their regular life. Various interviews of the team members back on earth are shown, including more information about the trip prior to the launch. Going forward again to the 19th month of the mission, team captain William Xu and Daniel confront Andrei about his slow recovery and after he leaves rather rudely the two decide that they will be taking him with them in the lander to Europa.
21 months, 16 days and 23 hours into the trip Jupiter is very close and pilot Rosa records in her video diary that the closeness of the planet brought back the excitement, and the team is ready to work for the mission again. The crew soon reach Europa and prepare the lander. They reach close to the surface smoothly but face radiation interference close to the landing site and choose an alternate landing zone about 100 meters away from the Conamara Chaos- their preferred site. Back on Earth at that time Dr. Umber still had no idea about what happened to the crew, and stared at Jupiter in the night sky hoping that they made it. Dr. Sokolov (Dan Fogler) informs again that the objective was to do extensive surface tests with a robotic arm to find life that would have been possible had they landed at the preferred site. At 22 months Daniel says it will be difficult to get the samples that they wanted since they did not land where they were supposed to. Dr. Petrovna suggests they should investigate under the ice since there is nothing else they can do. At 22 months, 1 day the whole landing craft shakes violently twice. Andrei is up in the cockpit and after the camera there gets interrupted by radiation, Andrei peeks out his window and then quickly grabs his camera to record something. While the team below is investigating the cause of the frequent ice shifts, Andrei climbs down and says, "Guys I saw something." Andrei reports he saw a light about 100 meters out and it was like an LED down with refraction, and it definitely moved. The team investigate feed from various cameras but cannot find anything, although they do notice radiation interference in all of the ships cameras. Daniel believes Andrei might have imagined the light, but Dr. Petrovna says it might also be the first indication of exactly the thing they came here to find. The team still worries about Andrei's condition and Rosa describes the teams emotions as a raw mix of awe, excitement and fear.
At 22 months and 3 days the ice drill finally breaks through to the ocean below. The team is very excited and wants to explore immediately by putting in a submarine probe. They are filled with awe seeing the beauty of the completely untouched environment. Dr. Petrovna the marine biologist is especially overwhelmed. They try to head to the target zone but also notice thermal activities closer than expected. The ocean is a 100km deep. The team is excited to find any signs of life. The thick layer of ice above prevents any radiation from interfering with the data but when even then they get a radiation spike, Dr. Petrovna figures it's coming from below, from much deeper into the target zone. The team prepares to readjust course, but as the radiation spike continues, they see a flicker of light and then something hits the probe lens, smashing it. The team loses control of the probe; the only way to get sufficient samples now is a surface walk 100m to the target zone. The team break into an argument because the radiation from Jupiter makes this very risky and yet this is the only way they can get samples.
Going back to 3 days, 8 hours and 38 minutes into the mission, engineer James Corrigan is alive and challenges that no life will be found in Europa. 6 months, 16 days into the mission, James records in his video diary how tough it is getting for him to stay focused. While the team continues with their daily duties, a solar storm hits the spaceship, damaging key components including communications. Their contact with earth is severed. This explains the image of Rosa in the cockpit being the last image received back on earth. What Earth doesn't know until later is that James and Andrei go out in their suits to fix several things across the ship. When they reach the communications panel Andrei tries to pry open a circuit board despite James' unwillingness and tears a whole in his suit's glove. Rapidly losing oxygen, he somehow manages to hold it with the other hand. James pulls him to the airlock to the decompression chamber, but Andrei was losing oxygen rapidly and seconds away from losing consciousness. Just when they are about to enter, James notices hydrazine spread all over his suit from the panel explosion. The chemical is very toxic and will contaminate the ship's environment, so he can't enter. Captain Xu tries to keep calm and asks James to push Andrei in before he dies, and they will come for James later. The veteran Andrei, on the verge of unconsciousness, tells James to get out of the suit and that he can make it into the decompression chamber without the external suit. Andrei won't go in without him. Andrei becomes unconscious due to depleted oxygen and James, after a moment of hesitancy, pushes Andrei in. The two astronauts are no longer tethered together and James in his hurry with Andrei forgot to tie himself to the hull. The ship drifts away and James is left with only minutes of oxygen. Captain Xu says he can no longer be rescued, because by the time they get to him, James will be lost. All he can do say he's sorry. James says it was an accident, and although terrified, he tells them to thank Andrei (still unconscious) for trying to save his life. He remembers his family, tells them goodbye and slowly asphyxiates to death. Andrei regains consciousness in the decompression chamber, and howls in despair on realizing what must have happened.
On Europa again, the team debates the possibility of a surface walk. Dr. Katya Petrovna volunteers and is very excited to do it. The 5 member team decides to vote. It's an even split save Rosa; she votes yes and Katya suits up for the walk. Once outside on the surface of Europa Katya can't believe she is there. She is filled with awe. Rosa climbs up to get a direct view of her from the cockpit window. On her video diary Rosa says saying yes seemed to be the right thing to do, and describes Katya's one hour excursion as a seeming eternity. On the surface, Katya sends back data from several samples. All are negative for life, but when she analyses a subsurface specimen, the team detected an unicellular organism. They can't believe it: Europa 1 has detected life outside Earth. William calls her back, but Katya sees a luminescence in a dark area that she thinks might be the one Andrei saw earlier. On her reserve oxygen she goes in to investigate. On reaching the area they again notice radiation spikes. Katya turns off her lights to see if the blue light she is seeing under the ice responds, and the luminescence shifts closer. The radiation interference spikes, and the crew advise her to get back inside. She is too curious, and as the luminescence quickly spreads around her she can't hear anything the team says. In a world of confusion she slips and the team is horrified to see her signals coming from underneath the ice. She is sinking and they can do nothing. On Katya's helmet camera feed, only her face is visible, her eyes wide with horror and a pulsating blue light all around her while she sinks deeper into the ocean. The team only receives static, and then nothing.
The death of Katya knocks the wind out of the team. They stipulate that the reaction of the luminescence to Petrovna's light suggests a complex organism, and they have to leave for Earth to let everyone know of the discovery, without further understanding of this organism, lest they all die and the news of their discovery is lost.
22 months, 12 days and 6 hours into the mission, the team attempt lift-off from the surface of Europa. Things go wrong from the start; the lander stalls and hurtles back towards the surface. While they are falling Captain William Xu gets out of his seat and tries to release the water shield to slow them down and soften their landing. He is successful and saves the crew, but is killed on impact.
After the ship's cameras come back online we see that Rosa, Daniel and Andrei are still alive; Captain Xu's last moment of bravery saved them all. Andrei does a damage assessment and it's not looking good. They are losing both heat and oxygen,and he predicts they will freeze before they asphyxiate. In hopes that the propulsion system is still intact, the team quickly goes into action. Daniel however quickly loses all hope as he realizes the ice under the ship is melting quickly. On her video log Rosa says it quickly became obvious that they had somewhat ironically landed in their original target zone where the ice was much thinner and constantly shifting. Andrei declares that it will take two men to work on the engines outside for two hours to get the engines back. Rosa suits the two guys up and says in her video log "that was that and that brings us to now...." It is now revealed to the viewers that the video log Rosa has been seen to be recording the entire time was only started after Andrei and Daniel set out to try and repair the lander's engine. Rosa records this video "just in case" they don't make it, hoping someday it is recovered by future explorers. She connects the recorder to the comm panel.
Immediately on opening the hatch, Daniel's suit camera catches radiation interference. He tries to descend using the skewed ladder and when he reaches the surface the ice underneath him gives away. Rosa loses contact with him and Andrei reports he was surrounded by blue light and then disappeared under the ice. Daniel is lost. Rosa asks Andrei if there is still hope and Andrei says says yes, but not for them getting off Europa. Andrei says he can fix the communications module by salvaging parts from the life support, so that they will be able to send their data to Earth. Rosa steadies herself to accept that they have to die and proceeds as per Andrei's instructions. Andrei reaches the surface without trouble and starts to transfer parts from the life support system to the communications panel. A blue luminescence appears right behind him underneath the ice. Rosa spots it with the lander cam, but there is severe radiation interference. The light starts to come closer to Andrei but he manages to finish his job. The lander goes mostly dark inside and the comm panel jumps to life. Rosa immediately starts uploading James' and her video diaries, along with all other on deck and external camera data, and data from the sample analysis. The ice underneath Andrei breaks and he falls, reporting in his last moments that the ship is about to sink. Rosa, in the cockpit, keeps the camera pointed behind her as the ship sinks below the ice. As she watches, crouching in the pilot's seat, the ship fills with water. Lights are seen moving under the surface, attached to some sort of tentacle. The last image seen is a that of an enormous octopus-like bioluminescent creature, closing in on the camera.
Mission director Dr. Unger explains how she got the final images and how their mission has finally come back to them. She says they witnessed the sacrifices made and the lengths the team went to push the discovery further. Dr. Unger reveals that in the last moments in the lander Rosa decided to open the hatch to let everyone see what might potentially be there. The discovery of the creature was beyond their most farfetched theoretical models and only shows how our universe is far stranger and far more alive than ever imagined.
The movie ends with a group picture of the whole team taken near the beginning of the mission, smiling and excited.