The film begins with a timeline, which states that in the future Earth has grown overpopulated and humanity has fought over the last natural resources. In the year 2174, a ship called Elysium was sent out to colonize an Earth-like planet called Tanis. In space, we see the massive ship flying towards the stars. On the bridge of the ship, we see officers receiving a message from Earth. The message is youre all thats left of us.

Next, we see Bower (Ben Foster) wake up from his hyper-sleep pod. He manages to free himself from the pod and rips out the tubes going into his body. He sees that he has a series of numbers tattooed on his arm. After peeling away his dead skin, he sees that he is alone. He reads that memory loss can be a side effect of long-term hyper-sleep. Not knowing whats going on, he finds a locker with his name on it and puts on some clothes. He finds a picture of his wife. He notices a couple of other pods are nearby. A pod for Cooper is empty. Another pod still has Payton (Dennis Quad) inside. Bower tries to wake Payton up by slamming something against the sealed pod, but hardly makes a scratch on it. He tries to open the door of the room but its locked. A power surge shakes the ship, causing Payton to wake up. Both men suffer from memory loss. Payton is a Lieutenant and Bower is a Corporal. It turns out that since the trip to Tanis would take over 100 years, the crew has been split into groups/shifts to work. At the end of a groups turn (after a couple of years), they are supposed to wake up the next group and debrief them. They realize that somethings wrong since theyre all alone. The numbers tattooed on their arms indicate which group they belong to. Another power surge shakes the ship, and Bower realizes that hes the engineer. Somethings wrong with the reactor and he needs to fix it. Payton gets a nearby command center working by using the auxiliary power. He tries to call for help but no one answers. They hear a noise coming from a nearby vent.

Payton decides that they need to find any crewmembers and get to the bridge to see whats happening. He sends Bower to find a way out in the vents while he stays behind at the command center to guide him around the ship. The vents are filled with tubes and are hard to crawl through. Bower tries to find his way to another room, but the vents look endless and run in every direction. After feeling like hes going in circles, he panics and becomes claustrophobic. Payton via radio calms Bower down by joking that he got the door open. Bower falls down a shaft and lands face-first on a grate. The fall causes him to lose contact with Payton. Bower turns on a glow stick and sees that Coopers decomposing corpse is right next to him. He falls through the grate and ends up in a storage compartment. Bower gets up but still cant communicate with Payton. The ship corridors are long and dark. While searching around, Bower comes across a woman trying to open a door. He tries to talk to her, but she quickly runs away. While chasing after her, he sees that she has seemingly stopped in a corridor. He tries to tell her that hes part of the crew and he needs to know whats going on. She remains silent. He shines his light on the figure and sees that its not a woman but a man; a man who has been hung and is missing most of his lower half. The woman, Nadia (Antje Traue), pops up and attacks Bower. She holds him down and orders him to remove his shoes. Suddenly, they both hear screeching nearby.

Nadia runs away while Bower is left confused. He sees a blue light at the end of the corridor and the screeching gets louder. The blue light is attached to a creature, which goes after Bower. The half-eaten man is pulled up and devoured. Bower runs back to the room he came through and hides in the storage compartment. While the creature looks for him, Paytons voice comes through the radio. The creature tears open the compartment and snatches Coopers body. After the creature leaves, Bower tells Payton that something not human is onboard the ship. Bower then remembers his wife and that families of the crew were allowed to travel on the ship. Bower becomes desperate to find her before the creatures do. He also remembers that Payton has a wife as well. Payton tries to convince him to continue making his way to the reactor. If Bower can fix it, the power will come back on for the ship and they can implement security measures.

Bower looks around and finds a security room. He finds an anti-riot gun and straps it to his arm. He goes into the corridors again and sees a hanged man. He thinks that hes going crazy since it looks like the same hanged man from before. However, upon closer inspection he finds that the man is different (hes still alive and in one piece). Bower cuts him down and is introduced to Shepard (Norman Reedus). Shepard is part of another group and has been by himself for a long time. Bower says that his commanding officer wants to know whats happening. Shepard says that there is no commanding officer and covers himself in oil to cover his scent from the creatures. He tries to leave but sees blue lights coming towards them. The creatures chase Bower and Shepard through the ship. The creatures are fast and have sharp weapons. They eventually string Shepard back up and eat him. Bower tries to shoot the creatures, but his shot is blocked by a door. The creatures see him and chase after him. He runs into Manh (Cung Le), who helps him escape from them. Bower cant understand Manhs language but still manages to communicate that hes part of the crew. He sees Manhs tattoo and sees that hes part of the agriculture crew. He tells him that hes going to start up the reactor and tells Manh to stay put. Meanwhile, Payton starts to get a bloody nose and gets increasingly scared that he cant talk to Bower.

Bower finds a large cargo container that acts as a living quarters. He sees that there are several other containers as well. Bower is attacked by Nadia again, who pins him down and threatens him with a knife. Manh pops up and defends Bower. As Nadia and Manh fight, Bower fires off a shot into the air. He tells them that he understands they want to survive, but to do so they need to stay together as a team. Come to find out, Nadia speaks English and eventually agrees and the trio makes their way through the ship. Bower tells Nadia that they need to start the reactor or else theyll lose everything. Nadia says that no one has ever come back from the reactor room. However, since she knows the way, shell lead him to it. They come across a hallway and find themselves surrounded by creatures. A power surge shakes the ship, allowing Nadia to activate a door open. They barely make it inside and seal the door. Nadia has been living in this room since she woke up. Shes a biologist and says that the ship is pretty much like Noahs Ark. In addition to the 60,000 people on board, there is DNA stored for all the organisms found on Earth.

After a while, Nadia leads the team through a part of the ship that holds civilian pods. Bower notices that the majority of the pods are empty. Nadia tells him that its the creatures feeding ground and tells them to hurry. Bower wonders if his wife is there, but Nadia tells him that the families of the crew are held in another area of the ship. Bower suddenly disappears. Nadia walks over to where he was and falls down a grate. Bower lights up a glow stick and they both see that theyve fallen into a massive pit of bones and gore. The creatures appear above the grate and move through the area. Bower climbs out of the pit first but keeps Nadia at bay. While he looks around, hes attacked by a creature. Bower is thrashed around and Manh comes to defend him again. He stabs the creature in the head, but its still alive. Nadia manages to stab it in the leg but is thrashed around as well. Bower manages to stab it in the chest, and the trio repeatedly stab it until its dead. The other creatures come back and see them. It screeches to its mates and some jump on the defeated creature and begin to devour it while others give chase to the trio. They come into another area and witness a man wake up from his pod. Bower attempts to help him but is too late as the man is stabbed in the head and eaten by the creatures. The team takes refuge in a room and seal the door shut.

Meanwhile, Payton continues to hear more and more noise coming from the vent. He grabs a pipe and climbs up. As he enters the vent, through the mass of hoses and wires, he sees a human arm reach out for him. Gallo (Cam Gigandet) is naked and covered in blood/slime and Payton pulls him through and locks the vent. Gallo says that he came from the bridge before passing out.

Back to Bower and his team. They find that they are not alone. Leland (Eddie Rouse) has been living in the room for some time now. Leland is situated on a balcony above the team so that they cant reach him. He makes them some food and welcomes them to his home.

Back to Payton; Gallo is passed out. Payton inspects his arm and sees that hes part of the previous group. Gallo wakes up and asks Payton what hes doing. Some of the blood on Gallo is from someone else, which makes Payton suspicious. Gallo says that he was with two other crew members, but they suffered from pandorum (i.e. space madness) and he was forced to kill them. Payton loads a needle gun with a shot to calm Gallo down, but he refuses to take it and becomes hostile. He accuses Payton of having pandorum and insists that he need the shot instead.

While Nadia bandages a wound, she tells Bower that she thinks the creatures are actually mutants. In all the hyper-sleep pods, everyone was supplied with an accelerator that was supposed to help them adapt to Tanis . Instead, it couldve made some people mutate and adapt to the ship.

Gallo tells the story to Payton about how Earth was destroyed and the thousands of people on the ship are all thats left of humanity - Leland tells the team what happened afterward. After Elysium received the final message from Earth (youre all thats left of us) and the team (which consisted of himself and Gallo) learned of its destruction, one of the crew members suffered from pandorum. He killed his crew and then started to wake people up. He ruled over them believing himself to be God. Whenever someone disobeyed him he would banish them to a lower part of the ship. Eventually, he grew tired of this and went back to hyper-sleep. However, over time the people he banished evolved/mutated into flesh-hungry creatures and adapted to the ship. As Leland tells his story, he fills the lower room with gas, knocking everyone out.

Bower wakes up to find himself, Nadia, and Manh hung upside down in the room. Leland plans on eating them for food. Nadia mouths off and Leland stabs her in the chest. Hes about to filet her when a power surge shakes the ship. Bower tells him that it was the last power surge. If they dont start the reactor within the hour, everything in the ship will shut down for good. Leland cuts them down and makes them walk through the ship at gunpoint.

Meanwhile, things get heated with Gallo and Payton. Gallo thinks that they should evacuate the ship while they still can, but Payton is confident that Bower will fix the reactor. Gallo insists that Payton is starting to exhibit signs of pandorum. Payton says that Gallo is crazy and continues to order him to "stand down".

The team comes across the part of the ship that holds the pods for families of the crew. Bower remembers that his wife isnt on the ship. He wanted her to go with him, but she refused. She left him, which caused him to sign up to be the engineer. He sees the pod for Paytons wife and remembers her name. He also remembers something else about Payton....