In 2008 Jason Voorhees is captured by the U.S. government and is being held at the Camp Crystal Lake Research Facility. In 2010, Rowan LaFontaine, a government scientist, decides to place Jason in cryogenic suspension after several unsuccessful attempts to kill him. However, Rowan's superiors hope to conduct further research into Jason's rapid cellular regeneration and instead try to take Jason. Jason breaks free from his restraints and kills the team of soldiers meant to transport him. Rowan successfully lures him into a cryonic pod and activates it.
However, Jason ruptures the pod with his machete and stabs Rowan in the abdomen, spilling cryonic fluid into the sealed room and freezing them both. In the year 2455, Earth has become far too polluted to support life and humanity has moved to a new planet, Earth II. Three students, Tsunaron, Janessa, and Azrael Benrubi are on a Field trip led by Professor Braithwaite Lowe who is accompanied by an android, KM-14.
They enter the Camp Crystal Lake Research Facility and find the still frozen Jason and Rowan LaFontaine, whom they bring to their spaceship, the Grendel. Also on the ship are Lowe's remaining students, Kinsa, Waylander, and Stoney. Once there, they reanimate Rowan while Jason is pronounced dead and left in the morgue. Lowe's intern, Adrienne Hart, is ordered to dissect Jason's body. Lowe, who is in serious debt, calls his financial backer who notes that Jason's body could be worth a substantial amount to a collector.
In the morgue, Jason comes back to life killing Adrienne by sticking her head in a sink filled with liquid nitrogen and smashing it against a counter top. Jason then takes a machete-shaped surgical tool and makes his way through the ship, killing Stoney, the pilot, and a contingent of soldiers led by Sgt. Brodski. With no pilot, the ship crashes through a nearby space station, damaging one of the Grendel's pontoon sections. Jason breaks into the lab, reclaiming his machete and decapitating Lowe.
With the ship badly damaged, the remaining survivors head for Grendel's shuttle, while Tsunaron heads elsewhere with Kay-Em 14. As the shuttle is being prepped, Jason intercepts them. On board the shuttle, Kinsa has a panic attack and launches the shuttle without releasing the fuel line causing it to crash into the ship's hull. Suddenly, Sgt. Brodski attacks Jason, but is easily overpowered. Tsunaron reappears with an upgraded Kay-Em 14, complete with an array of weapons and new combat skills.
She fights Jason off and seemingly kills him, knocking him into a nanite-equipped medical station, and blasting off his right arm, left leg, his left rib cage and finally part of his head. The survivors send out a distress call and receive a reply from a nearby patrol shuttle. Nearly an hour passes, as the survivors begin setting explosive charges to separate the remaining pontoon from the main drive section. As they work, Jason is brought back to life by the damaged medical station.
Since much of his biological tissue was destroyed, he is rebuilt as an even more powerful cyborg. Jason then easily defeats Kay-Em 14 by punching her head off. As Tsunaron picks up her still functioning head, Jason attacks them, but is stopped by Waylander, who sacrifices himself by setting off the charges while the others escape. Jason survives and is blown back onto the shuttle. He punches a hole through the hull, sucking out Janessa. A power failure with the docking door forces Brodski to go EVA to fix it.
Meanwhile, a hard light holographic simulation of Camp Crystal Lake is created to distract Jason, but he sees through the deception just as the door is fixed. Brodski confronts Jason so the rest can escape. As they leave, the pontoon explodes, again propelling Jason at high-speed towards the survivors.
However, Brodski intercepts Jason in mid-flight and maneuvers them both into the atmosphere of Earth Two, apparently killing them both. Tsunaron assures Kay-Em 14 that he will build a new body for her while Rowan breathes a sigh of relief. On the planet, two teens beside a forest lake set off to find where a "falling star" landed as Jason's mask sinks to the bottom of the lake.