While exploring the far reaches of space, Logan, along with his new friends, Palladon and Rae, discover the commercial towing spaceship Nostromo is on a return trip from Thedus to Earth at some point in the future, hauling a refinery and twenty million tons of mineral ore, and carrying its seven-member crew in stasis. Upon receiving a transmission of unknown origin from a nearby planetoid, the ship's computer awakens the crew. Acting on standing orders from their corporate employers, the crew detaches the Nostromo from the refinery and lands on the planetoid, resulting in some damage to the ship. Captain Dallas, Executive Officer Kane, Navigator Lambert, Logan, Rae and Palladon set out to investigate the signal's source while Warrant Officer Ripley, Science Officer Ash, and Engineers Brett and Parker stay behind to monitor their progress and make repairs.
Dallas, Kane, Lambert, Logan, Rae and Palladon discover that the signal is coming from a derelict alien spacecraft. Inside it they find the remains of a large alien creature whose ribs appear to have been forced outward from the inside. Meanwhile, the Nostromo's computer partially deciphers the signal transmission, which Ripley determines to be some type of warning. Kane and Palladon discover a vast chamber containing numerous eggs, one of which releases a creature that attaches itself to Kane's face. Dallas, Lambert, Logan, Rae and Palladon carry the unconscious Kane back to the Nostromo, where Ash allows them inside against Ripley's orders to follow the ship's quarantine protocol. They unsuccessfully attempt to remove the creature from Kane's face, discovering that its blood is an extremely corrosive acid. Eventually the creature detaches on its own and is found dead. With the ship repaired, the crew resume their trip back to Earth. In an attempt to save Kane, Rae uses one of her healing charms to save his life.
The result of Rae's spell causes Kane to awaken seemingly unharmed, but during a meal before re-entering stasis he begins to choke and convulse until an alien creature bursts from his chest, killing him and escaping into the ship. Lacking conventional weapons, Logan's team and the crew attempt to locate and capture the creature by fashioning motion trackers, electric pods, and flamethrowers. Brett follows the crew's cat into a large room where the now-fully-grown Alien attacks him and disappears with his body into the ship's air shafts. Dallas enters the shafts intending to force the Alien into an airlock where it can be expelled into space, but it ambushes him. Lambert implores the remaining crew members to escape in the ship's shuttle, but Ripley, now in command, explains that the shuttle will not support four people.
Accessing the ship's computer, Ripley discovers that Ash has been ordered to return the Alien to the Nostromo's corporate employers even at the expense of the crew's lives. Ash attacks her, but Logan and Parker intervene and decapitates him with a blow from a fire extinguisher and Logan's keyblade, revealing Ash to be an andriod. Before Palladon incinerates him, Ash predicts that the other crew members will not survive. Logan's team and the reamining three crew members plan to arm the Nostromo's self-destruct mechanism and escape in the shuttle, but Parker and Lambert are killed by the Alien while gathering the necessary supplies and Logan and Rae arrive to find Palladon unconscious, after a failed attempt to defend the crew. They meet up with Ripley, who initiates the self-destruct sequence and heads for the shuttle with the cat, but finds the Alien blocking her way. While Logan and his friends take on the creature alone, she unsuccessfully attempts to abort the self-destruct, then returns to find the Alien and her friends gone and narrowly escapes in the shuttle as the Nostromo explodes.
As she prepares to enter stasis, Ripley discovers that the Alien is aboard the shuttle. She puts on a space suit and opens the hatch, causing explossive decompression which forces the Alien to the open doorway. She shoots it with a grappling gun which propels it out, but the gun is yanked from her hands and catches in the closing door, tethering the Alien to the shuttle. It attempts to crawl into one of the engines, but Ripley activates them and blasts the Alien into space. The last that Logan and his friends hear from Ripley, following their own escape, is her final recording just as she joins Jones in stasis. Feeling guilt-ridden for their loss and for almost putting his friends in danger (Despite all their experience), Logan decides to drop Palladon and Rae back to their "own time" on Earth and continues his voyage in space alone as his friends watch on.
- The scenes where Ripley, Logan and his crew witness Brett being dragged into the air shafts by the Alien and where they find Dallas and Brett cocooned in the bowells of the ship are nods to two infamous deleted scenes from the original movie, which were included (although recut to be more streamlined) in the 2003 director's cut.