The crew of the Nan-Shan Industries colonial ship Forecastle, led by Captain Alistoun, is woken by an odd distress call in the deepest reaches of space. It carries hundreds of sleeping colonists in the vast hold and a small crew to man its hauler, the Sea Child (which also doubles as a land-to-surface vessel as with the Nostromo).
When they awaken, the crew detaches the Sea Child from its umbilicus with the Forecastle, leaving their human cargo behind, to explore the source of the signal without risk to their payload. They find a battered and burned Sulaco, having drifted for over 200 years into the furthest reaches of space. They board and find three eggs. Two look dead. The third, though open, is fresh. It's opened very recently. Onboard, they also discover basic robot drones that are still active, and which initially try to bar entry to the bridge and central computer, until they are destroyed.
After exploring the vessel, one of the crew, Wait, is impregnated and subsequently put into stasis. Wait, who had recently been diagnosed with an aggressive cancer of the lymphatic system and spinal cord, initially seems to get better - but his partner, Dr MccWhirr, is worried about the presence of the strange new 'tumour' growing inside him so freezes him. Hacking into the Sulaco's mainframe and black box, MacWhirr sees the queen from Aliens placing three spores that grow into eggs. She also gets bits and pieces of information about the alien, and how it transforms its host like a virus. She suspects there may be a way to use the parasite to her advantage and save Wait.
She and the crew trace the Sulaco's progress back to LV-426, where they think they might be able to get some clues about how to help their colleague and rid him of his 'infection'. They all go into quarantine, and though they re-connect with the Forecastle, they activate the quarantine protocol to make sure to keep their human cargo safe and separate (locks and failsafes keep them sequestered).
Meanwhile, one of the crew, Singleton, a secretive type, pulls off a mole on his arm and connects himself to the ship computer. He sends out a message unbeknownst to his friends.
Shortly after, some members of the human cargo wake aboard the Forecastle unexpectedly, and find themselves physically separated from their crew and the bridge by a corridor of sealed doors. Their comms have also been deactivated, as if the central computer has locked them in without any way to escape or communicate. The cryotubes, they realise, have been deactivated and will not power up. Something is very wrong.
They realise the quarantine protocol has been activated, keeping them trapped, and because they can't get any messages to the bridge believe they have been awakened by a computer error or some other technical accident (they don't want to acknowledge the idea of sabotage, as it scares them more than their current predicament). Knowing that they are several years from their destination, without sufficient food or water to survive in their cryo suite and adjoining locker rooms, colonist Donkin comes up with a plan to get into a space suit, blow the airlock, and use squirters to propel himself to the bridge of the Sea Child so he can cancel the quarantine protocol and help his follow passengers escape their imprisonment.
Returning to LV-426, Alistoun's crew finds the planet is a scorched wasteland and there's nothing there to help them. The supposed medical unit on the planet was long ago wiped out. While discussing what to do next, a siren blares: PROXIMITY ALERT! Looking at the scanners, a ball of rock or metal seems to be heading right for the Forecastle. It's too close for their weapons to take it down. Alistoun recommends manoeuvring to avoid collision. Through a viewport, we see the ball unfurl, revealing the queen from Aliens, who has been in hibernation like a tardigrade since Ripley ejected her into space.
Then we cut to a new ship: the Betty. Shooting through space towards LV-426 and towards the Sea Child/Forecastle nearby. Ripley and Call board the Sea Child to find a new hive has developed onboard the Forecastle. Somehow, an airlock was blown and the queen got onboard, Captain Alistoun explains. The queen then impregnated the revived passengers in the first cryo-chamber and escaped into the interminable ducts to build her hive somewhere.
A few survivors have holed up in the Forecastle, and they finally manage to contact the crew of the Sea Child. Alistoun communicates this to the Betty crew, and Singleton reveals he is an auton and contacted Call (having heard of her 'outlandish' claims of space beasts through the underground networks).
Ripley, Call and the crew of the Sea Child must find the hive in the Forecastle and destroy it without harming or exposing any of the other sleeping passengers. Meanwhile, they have to deal with an ancient W-Y AI which had been operating on the Sulaco's main computer (it was this AI which had awakened the eggs there by use of its onboard machine drones) and which has infected the Sea Child and Forecastle. It is the AI which awakened the colonists in the first chamber, and MacWhirr may or may not have been helping it to save her partner (at first it will certainly seem that way, but I may have her be innocent after all).
Ripley, who has begun dreaming of the aliens again, especially of herself transforming into an alien queen, has an idea: to make herself an alien suit and enter the hive. She uses a dead drone to do this. She hopes her queen DNA will allow her to enter the hive safely, and that she can control the aliens with her own pheromones. Meanwhile, Call and Singleton must enter the mainframe and destroy the Sulaco AI.
Ripley enters the hive and manages to get to the queen, whom she challenges to a fight for control of the hive. The praetorian guards allow this to happen, as it's common for rival queens to duke it out in this way. Ripley, of course, is no physical match for the queen, but has some tricks up her sleeve.
When the queen attacks, Ripley is able to use a sound cannon Call has been developing to block the aliens' higher frequency communications. This causes the queen intense pain, and hurts Ripley too, but Ripley has noise dampening earplugs which help her push through the pain. She kills the queen and, taking the role of the new queen, commands the drones to plunge headlong into the fusion drives, killing them all for good.
Emerging from the hive, the rest of the crew and passengers now safe, Ripley says she experienced a vision during the moment the sound cannon kicked in: the original homeworld of the aliens, and a queen above queens, from who all the other aliens came. She convinces the crew of the Betty to set off with her for one final showdown with the creatures, and the credits roll with the Betty flying off into deep space...
So it's an early draft, but I've tried to structure it to mirror the first two movies, and draw upon some of my favourite elements from the comics and their novelisations. I've actually started writing this, just for fun, which is distracting me from my current novel, but I like it.
Ship and crew names above are taken from the works of Joseph Conrad. Specifically, The Children of the Sea, from which the name Narcissus was also taken.