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It is the year 2548, more than 300 years since Earth lost contact with the colony ship Ozymandias, en route to the distant planet, α2. Unexpectedly, the ship has reappeared in orbit over Jupiter. Earth sends the probe ship Seyfert to investigate, and it launches a shuttle carrying highly trained Special Operations And Reconnaissance (S.O.A.R.) operators to board the ship. Ozymandias then fires upon Seyfert, destroying it, before turning on the shuttle.

Four survivors make their way onboard Ozymandias: Patrick Tyler, Sonya Hart, McCoy, and their CO, Jacob Ranshaw. They must wait at least three days after they are declared over-due before they can expect a rescue party. Tyler, Hart and McCoy find themselves in the ship's hangar deck, where McCoy is killed by a Tyrannosaurus-like creature, Australis, which chases Tyler and Hart across the chamber before stopping its assault and hearing something rattling on the rafters. The beast is then ambushed from above, mauled, and killed by a pack of the eel-like Rigel, which eat it alive after one of them is ripped in half and thrown to the floor. They soon turn their fury onto Tyler and Hart.

Tyler and Hart are separated by the antics of the computer system, MTHR-248, though this allows Tyler to find Ranshaw, fighting Rigels, Algols, and a second Australis along the way. Debris from Seyfert destroys a window and the two men are almost sucked out into space, but Hart is able to force the emergency shutters down. The three continue their investigation, where they discover the original crew perished in 2248 from radiation poisoning, with the ship's CO Captain Satoko Evans ordering MTHR-248 to create clones of them in the ship's DNA Laboratory to save the mission, but for as yet unexplained reasons switched to creating genetically altered dinosaurs. However, the S.O.A.R. members have not seen any humans yet.

When an unidentified life reading is registered in the Storage Sector, Tyler heads out to investigate, soon running into a young woman, Caren. However, she flees from Tyler's sight. MTHR-248 tries to keep the two separate, going as far as to destroy the Storage Sector itself, but Tyler continues on, dismantling the Rigel's fortress, the Rigel Domain, and coming across a Kornephoros, which tosses some of the equipment across the room and beats its chest, along the way. Tyler tracks Caren down twice: first when she is harassed by a pair of Algols, and then to her father's quarters, discovering she is the daughter of noted cyberneticist Dr. Miguel Angel Velasquez de Silva, apparently surviving for three hundred years in a cryo chamber. Caren leaves Tyler behind, and he tracks her down once more to a Hologram Room displaying a recreation of the solar system. Caren has been warned by MTHR-248 not to trust Tyler as he is dangerous, something he confirms in his plans to shut down the computer system. Tyler is able to get her to see how MTHR-248's rampant behaviour is the true danger, and the computer responds by unleashing a surge of electricity in the room.

When Hart heads out of the ship to save Tyler and Caren, she discovers an escape shuttle on the aft section of the ship, which the group can use to leave immediately rather than wait for rescue. Hart and Ranshaw head over to the Shaft Sector to meet with Tyler, who begins his search of the DNA Laboratory. Tyler is attacked by a newly born dinosaur, a Regulus, which breaks free from the embryo tube and sets the room ablaze. Hart and Ranshaw's rescue goes awry when Caren gets involved, and is seriously injured when the beast delivers a crushing blow to the torso with its powerful tail, sending her flying to the wall. After ordering Hart and Tyler to leave the chamber despite Hart's protest, Ranshaw goes toe to toe against the beast, and after running out of ammunition, also suffers injuries, and kills himself with a grenade in an attempt to take Regulus with him. Outside of the DNA Laboratory, Caren dies and her skin turns to dust, revealing she was in fact one of Dr. Velasquez's androids the entire time. As Tyler travels on ahead, he drops down into the lobby, where the Regulus rolls towards him and looses a challenging roar. After slaying the beast and avenging Ranshaw, Tyler is shocked to find Caren once more greeting him, the new android having not only downloaded all the memories of the first, but unaware of her true nature.

Closing in on the escape shuttle, MTHR-248 causes problems to Ozymandias' Third Energy core, requiring Tyler to traverse the Shaft Sector once more, but in 0G, and through the Deck Sector as it begins to freeze due to a malfunctioning environment system. Tyler obtains the required Atomic Cylinder required to reactivating the core, almost being killed by a large foot crashing through the ceiling in the search. As the doors freeze over, Tyler is left trapped in the Hangar Deck, watched by MTHR-248, who sends in a surprise for him: a third Australis pops out from a nearby generater. Even after the beast is slain, Tyler is still unable to handle the cold tempeature. Realising he is in danger of dying in the cold, Caren uses her familiarity with the ship to thaw the section out. Tyler is able to insert the Atomic Cylinder into the Third Energy core, but another accident happens, this time risking the destruction of the ship. To make matters worse, the chamber floods, and an aquatic, water-breathing dinosaur known as the Miaplacidus crashes through the wall, knocking Tyler off the footbridge. After a short confrontation, the beast is forced to retreat.

Tyler, Hart and Caren reach the MTHR Sector as the aft section of the ship detaches itself from the rest, escaping the explosion and activating its Warp drive to take it straight to Earth orbit. Tyler heads up to the MTHR Room to shut down the computer system once and for all, and finally discovers the missing elements of the puzzle. The mutant dinosaurs were side-products in MTHR-248's research in creating a perfect human-dinosaur hybrid which could survive in any environment, existing to test out genes that would go into the hybrids. A dozen cloned foetuses have been created, ready to be sent to Earth, and each paired with its respective android to look after it. Suddenly, the chamber floods, and tile starts to move around. The Miaplacidus, having escaped to the aft section, cuts the tiling in its sail and jumps out of the water over Tyler. The beast is then slain when it falls into the water. MTHR-248 itself is damaged beyond repair and shuts down, its last words being that it wanted to complete its mission. Unfortunately, this proves disastrous, and Hart and Caren regroup with Tyler as the ships's self-destruct system sounds. As they leave the room, Caren spots the androids and realises her true nature.

Heading for the escape shuttle in the Engine Sector, the three are confronted by MTHR-248's most dangerous dinosaur, the dual tailed, two-headed Cebalrai, the adult form of Rigel capable of surviving in vacuum. After a chase down the walkway, Tyler is tossed into the wall by the beast and cornered; his gun is flattened in the process. Caren lures the creature to the side of a deep shaft, sending it and herself falling to the bottom, with Caren declaring she never belonged on Earth due to not being human - an act which greatly dismays Tyler. After obtaining a rear engine entry permit and slaying the fourth and final Australis, Tyler and Hart make it to the escape shuttle and launch, but are attacked once more by the Cebalrai, which made its way out into space and landed on the shuttle. Tyler decides to teach the persistent creature a final lesson. Midway through the fight, the beast generates a third head in between the first two heads, rending some of Tyler's guns ineffective. With the assistance of the Final Wasp, Tyler is able to throw Cebalrai off the shuttle, letting the creature spend its days floating aimlessly in space. Tyler comments that it is finally over before uttering Caren's name one last time as the shuttle sails down toward Earth.