Bower remembers that the woman he remembers is no longer his wife and isn't on the ship.
She left him and he had nothing left so him to sign up to be the engineer to found a place in history.
Meaning that she vanished along with Earth. Nadia who is grateful towards Bower for saving her life, tries to comfort him by saying she saved his life by leaving him. But he is consumed by grief which almost makes him give up on the mission.
However, Nadia gets him but on track saying that they were meant to go on and survive. He sees the pod for Paytons wife and remembers her name. He also remembers something else about Payton.... The team makes it to the reactor but find that below it is the sleeping ground for the creatures. Bower tries to walk across a catwalk to the reactor but it gives way. As Bower falls, he manages to get a grip on the catwalk. Manh holds onto the catwalk while Nadia runs across to help Bower.
However, Bower's hand slips and he falls, but he catches a large brace mid-way into the fall. He manages to climb down where the creatures are resting. Bower covers himself with skin/slime so that the creatures won't pick up his scent.
He then crawls amongst them to get to the ladder leading up to the reactor. Once he gets there, Leland accidentally drops a light down to where the creatures are, waking them all up.
Leland runs away while Manh drops the catwalk, crushing a couple of creatures. He makes noises and leads the creatures away from Bower and Nadia. Bower climbs up to the reactor and turns on the power, which fries some creatures in the process.
Gallo takes control of the needle gun and forces Payton to open his pod. Gallo has Payton start the ejection sequence and gets inside.
However, Payton tricks Gallo and instead just locks him inside the pod.
Elsewhere, Manh manages to elude the creatures but then runs into the leader. The leader tosses Manh a spear and they fight. The leader pins Manh against a wall and starts to eat his stomach. Manh grabs a knife and repeatedly stabs the leader in the head until it dies. Manh then turns around to find a creature child staring at him.
He contemplates killing the child, but lowers his knife. The child in turn slices Manh's throat open. Bower turns on the reactor, providing power to the ship (which opens the door to the bridge).
Payton is happy that Bower succeeded, but then finds that Gallo has escaped from his pod.
Gallo attacks Payton and they fight for control over the needle gun. During the fight, their arms merge together. It's shown that Payton is the only person there and has been fighting himself.
After Payton stabs himself in the leg with the needle, Leland winds up in the command center.
Payton promptly fires the needle gun into Leland's eye killing him. Bower and Nadia make it back to the bridge while being chased by creatures.
They lock the door and find Payton already there. Bower knew Payton's wife and knew the real Payton. It's revealed that "Payton" is actually Gallo! He was interacting with a younger version of himself (how he looked when he first started working on the ship) playing mind games with himself like he did with the passengers.
Bower remembers what the real Payton looks like and knows that Gallo is the "God & Devil" from the story.
When he went back to hyper-sleep, he got into Payton's pod instead of his own. Bower asks Gallo where exactly they are.
After opening the window shields, all they can see is darkness and Bower panics from claustrophobia feeling that there is no escape. This, the revelation of the fate of Earth, and his ex-wife is too much for Bower and the effects of Pandorum start to catch up to him.
It's revealed that Gallo has became so paranoid that has has turned into a misanthrope who favors anarcho-primitivism. Because human civilization had ruin Earth's resources with overpopulation, he has come to believe that life eating life like in the wildness is perfect. He tells Bower that with the ship they can create a new world with the ship (alluding to Nadia's theory) but in a wild primitive state.
Meaning that he purposefully created the creatures that now roam the ship. He now attempts to exploit Bower's descent into madness like he did with the paranoid passengers and convert him to savagery.
The flight log shows they have been on the ship for 923 years and realize that Elysium has been on Tanis the entire time, crash-landed in an ocean underwater. Nadia sees fish swimming past the ship.
The creatures are not the passengers, nor did the passengers mutated but instead they are their descendants who evolved into a subhuman species after generations of natural selection. Gallo then attacks Bower but Nadia tries to stop him but due her injury she is overpowered. Bower hallucinates about creatures trying to break into the bridge. Gallo grabs Bower and shoves him. Bower falls backwards into the commander's chair and Nadia tries to defend him.
Gallo throws her off and advances on her with a knife. Bower, still hallucinating, shoots a compartment (thinking a creature is coming through), causing a piece to crack the window. Bower grabs Nadia just in time to see the windows break, flooding the ship with water.
They run off and Gallo drowns. Bower and Nadia run back to Bower's pod. They both get in and seal the door shut, but a lot of water gets in as well.
Bower lets Nadia have his air mask while he almost drowns. The pod pops out of the surface of the ocean. Bower and Nadia survive and look around the alien planet. The ship, experiencing a hull breach, enacts the evacuation plan and ejects all the remaining pods. Soon the rest of the pods pop out of the ocean and the remaining people start to wake up. The film ends with text, stating that the population on Tanis year ONE is 1,213 people. Bower had found his place in history.
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