It begins with a shot of the hypersleep vault aboard the Nostromo, but it then cuts to a shot of Ripley, Lambert, Parker, Ash and Dallas discussing the Alien in the ship's mess hall following Brett's death. They figure that the Alien is using the ducts inside the ship to move around, and Dallas suggests leading the Alien to the main airlock. The player then gets to decide if Ripley, Parker or Dallas goes into the ducts. The player grabs a flamethrower, motion tracker, Maintenance Jack and possibly a flare and Medikit. They then meet with Ash, who tells them that the security systems has shut a number of doors, so they'll have to gather equipment en route. The player descends a ladder to B Deck, and Ash seals the hatch behind them.

While avoiding being killed by the Alien, the player seals maintenance hatches 00B1 and 00B2. They then pass through the landing claw bay, where Brett's corpse is located, and seal either hatch 00B3 or 00B4. After sealing the hatch, Ash tells them to find the primary air shaft system, and lead the Alien to C Deck. There, Ash can connect to the airlock systems from his terminal. After entering the primary air shafts, the player's motion tracker begins malfunctioning. Lambert finds the player on her motion tracker and tells them that the Alien is also inside the shafts. Lambert attempts to guide the player through the shafts while they avoid the Alien. Eventually, the player reaches the end of the shafts and drops down to C Deck.

The player then has to connect Ash to the airlock systems. Ash tells them that he's opening the outer airlock, but it'll take some time, so they should find somewhere to hide. Eventually, Ash informs them that it's primed, and instructs the player to wait for the Alien to enter the outer airlock chamber and be ready to close it in. Once the Alien enters the airlock, the player approaches the airlock and presses the button to seal the airlock. However, Ash tells them that something strange is happening, and the switch does not work. An alarm inside the airlock activates, and the Alien flees, knocking out the player. Once they wake up, Ash is waiting for them.

It ends with a shot of the med lab, as Ash's voice is heard delivering his iconic monologue from the movie: "Bring back lifeform. Priority one. All other priorities rescinded. You still don't understand what you're dealing with do you? Perfect organism. Its structural perfection is matched only by its hostility. I admire its purity. A survivor. Unclouded by conscience, remorse or delusions of morality. Last word. I can't lie to you about your chances. But... you have my sympathies."