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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 a². Somehow, the ship has reappeared near Jupiter. A team called S.O.A.R. (Special Operations And Reconnaissance) is sent aboard the probe ship Seyfert to investigate. A small team is sent off on a shuttle in an attempt to board the Ozymandias, when the ship's weapons power up and launch a laser at the Seyfert, destroying the ship. The weapons then direct themselves at the shuttle and fire, slicing it in half and destroying it.

Fortunately, Patrick Tyler; Sonya Hart; commander Jacob Ranshaw, and McCoy survive the blast. They manage to make it to the Ozymandias and board the ship. Inside the ship proves to be quite derelict, though there is still power.

Patrick and Sonya soon find themselves face to face with an Australis (A Tyrannosaur-like creature) which kills McCoy. The Australis is in turn killed by a small colony of the eel-like Rigel, which eat the Australis alive from the inside.

As Patrick, you fight your way through parts of the ship until you reach the Bridge, where one life-sign is discovered somewhere in the ship. You are sent out to investigate. After fighting your way through the ship's storage areas, you finally meet the surviving human, a girl by the name of Caren Velasquez. After defeating a horrifying planet-like organism, Patric is forced to make a hasty retreat as the Ozymandias' MTHR - the ships control system- ejects the entire storage sector from the ship in hopes of stopping Patrick.

After finding his way through the rather confusing Shaft sector, Patrick meets Caren, and reveals that she reminds him of his sister, and that he feels the need to protect her. Patrick reaches the top of the Shaft sector, where he is attacked by a large Regulus. Luckily, Sonya and Jacob this time manage to save Caren, who was injured. Jacob is next to be rescued. Jacob then fights the Regulus head-on, sacrificing himself by detonating a grenade, destroying the room and everything in it. Patrick, Sonya, and Caren manage to escape just before the detonation. Caren soon dies, revealing that she is not, in fact, human, but is instead an android.

Unfortunately Jacob's sacrifice was in vain though, forcing you to fight the large dinosaur anyway. Upon defeating the Regulus, Patrick sees a "new" Caren running through a hatchway.

After restarting the Ships core in the Energy Sector, Patrick is forced to head back after a problem causes some parts of the ship to malfunction. After making it through the Shaft Sector in zero-gravity, Patrick then gets through the Deck Sector with malfunctioned Environmental Systems. On his way to the Hazardous Waste Storage Room, which contained an item to repair the ship, Patrick is almost crushed by a huge foot going through the ceiling. After being forced to the hanger deck after previous rooms froze the doors shut, MTHR has a surprise for him.

After another confrontation with an Australis, Caren manages to repair the ship, saving Patrick from succumbing to the broken environmental systems. Patrick then goes back to the Energy Core to restart it, but the room is severely damaged after MTHRs aquatic creature, "Miaplacidus," crashes through the wall, filling the area with water coolant.

When the fight is finished, the Creature escapes and the trio run to the MTHR sector as the core begins to go into meltdown. As the trio arrive at the sector, the MTHR and Engine sectors detach from the Front Deck, Shaft and Energy Sectors, which are destroyed by the meltdown. The Engines soon activate an emergency system and Warp jump to Earth.

Patrick tries to stop MTHRs main computer but she opens another hatch releasing Miaplacidus a second time. Upon defeating the creature, Patrick tries to stop M.T.H.R. sending the dinosaurs to Earth and fights her, eventually destroying her system, which has disastrous effects on the ship, causing it to activate the Self-destruct.

Patrick is reunited with Sonya and Caren as they try to escape the ship via an escape shuttle, but they are attacked by the "Cebalrai", an adult Rigel. Patrick is then attacked by the creature, being unable to reach his gun. Caren decides to sacrifice her self to make her self fall, along with the dinosaur from a collapsed platform. Patrick and Sonya are able to escape before the ship self-destructs. But the Cebalrai, being able to survive in vacuum, was able to get on the top of the shuttle. Then Patrick gets on top of the shuttle himself to destroy the "genetic freak", and so the final battle begins.

Midway through the battle, the Cebalrai grows a third head, and Patrick is forced to use a "Final Wasp," which weakens the creature and sends it flying into space. Upon its defeat, Patrick stands on top of the ship and says: "It's finally over! Caren ...". Then the Earth is shown on the screen where the game ends.