I got a bit stuck in the writing, I'm still about a third of the way through, I had a few things I had to make up a bit differently.
I also realized that my ending is pretty open ended and maybe strange. But I've decided to finish it as I have it figured out, and then see if I can rework it. Also, I may have spent an unnecessary amount of time thinking about how terraforming works, even though it's not necessary for the story.
Anyway, I'm going to post at least this first third of the story I've finished here now, so you can make up your own minds if my sequel is crap. For those who don't want to read the whole thing, I'll put a shortened version here, about four times shorter.
Ship
For my story I'm creating a professional space police unit, maybe something like the FBI or NCIS. Let's call it, say, CCIS, Cosmic Criminal Investigative Service. I'm not sure if it should be subordinate to any particular government or international organization. Then it would have an international name.
I also need a ship for the story, let's call it a Dragon class ship. It should be a small, fast, well-technology ship with gravity and anti-gravity technology that allows it to travel interstellar and also operate well in the atmosphere, for example, levitate noiselessly in the air.
(Gravity technology is present in the Alien universe at least as artificial gravity. Hypothetically, if g. technology were used in fusion reactors, I could imagine that the implosion of a gravitational field could produce an effect identical to the hydrogen bomb we saw in the movie Aliens.)
I tried to draw a plan of the ship to help me better plan the story. This ship should be equipped with everything needed in a small space, just like ambulances or fire trucks. And after my attempt, I have to say that it's quite hard to plan something like that, especially when I don't have a proper idea of what all the equipment would be needed. Just like I have no idea what all the equipment needs to be crammed into an ambulance. So, in the end, there are spaces in my ship that I don't have an exact purpose for.
Well, here's the result. 85 metres long, 20 metres wide, about 12 metres high. I was expecting it to be smaller, but the Sulaco, for example, is claimed to be 385 or 731 metres long, and the Nostromo 244 metres.
This is a plan of the lower deck where the crew will be moving. The upper floor contains other systems, such as life support, filtration, decontamination, sensors, transmitter, drone and space probe carrier, bridge system to connect two ships in space, maybe also emergency parachutes in case of gravity engine failure.
On the bottom of the ship there will be some additional sensors, weapons, an extendable landing gear and emergency thrusters in case of engine failure.
The ship has an advanced artificial intelligence, which the crew calls Auntie, as well as 10 robots that are able to work independently or remotely.

The first third of the sequel - SHORT VERSION
(The full version will be up when I run it through the translator.)
Part 01
The Cosmic Criminal Investigative Service has received a report from someone in Colonial Marines Command about suspicious activity by Weyland-Yutani and Colonial Marines. Two ships are dispatched, Dragon1 and Dragon2, each with a crew of eight. One to LV-426, the other to the prison planet Fury.
A civilian transport ship has also been called in, moving within range of LV-426, to wait nearby in case civilians need to be evacuated. The ship returns from the colonies and is nearly empty.
Dragon1's journey to LV-426 will take 15 days.
Part 02
Dragon1 is approaching LV-426. The civilian transport ship is already at the edge of the system.
Dragon1 flies in low orbit over LV-426 and acquires surface information. Radioactive crater where the Atmosphere Processing Plant (APP) and colony should be. An anomaly 35 to 38 kilometres from the epicentre, then further away what is probably a large vehicle.
There's a chance that some of the colonists survived if they're in that vehicle, or if they've taken refuge in a lava tunnel with enough supplies.
Dragon1 is descending into the atmosphere. It launches two winged drones at the crater rim to search for the colonists. Dragon1 then heads for the anomaly.
Part 03
The team discovers something unlike anything humans have seen before. They find formations of various shapes on the surface. What the Dragon1 crew doesn't know is that it is a Derelict, fragmented and scattered by a pressure wave and a missile attack from the Sulaco ship from orbit. However, they don't look like shredded pieces. They appear to have healed and reshaped themselves after being torn apart, and are re-growing back together, connecting with tubes and biomechanical roots. Creating a biomechanical landscape. (Similar to the ones we know from the works of Giger and also his fans.)
Spectral analysis shows a mixture of organic and inorganic elements. Further measurements show that the biomechanical formations suck in the atmosphere and let it out, free of carbon dioxide, like a plant.
The team is saving a more detailed investigation for later. The ship's AI Auntie interrupts them with a report that the drones' cameras have picked up an unknown animal near the crater, in a radioactive area. It is a hughunter. (I've already posted a picture here.)
The captain, unnerved by the discoveries, asks if all data are automatically sent to Earth, just to be sure. Of course they are. He then gives the order to proceed to the vehicle.
Part 04
Dragon1 flies over the target.
Below them is a large vehicle that is commonly used on other planets. It's long, larger than a shipping container, equipped with massive wheels and a hydraulic chassis.
A scan of the vehicle shows only two people lying inside, presumably asleep.
The team suspects they are not colonists, but rather criminals who need to be detained and interrogated.
The team sends two robots, using a government backdoor program to get inside. They quickly handcuff the first person.
The second person is inside a high-temperature waste incinerator. It's a humanoid figure covered in a layer of metallic grey-black shiny unknown matter. It doesn't look quite human, but it is breathing and has a heartbeat.
The shackled man is being transported by the first robot to Dragon1 in isolation.
Part 05
Scan shows it's not a human, but an unregistered android. The brain is synthetic, the body is organic. Very illegal.
More robots are sent to the vehicle. The interior looks like a well-equipped laboratory and a two-person habitation. The robots begin to sample the surfaces with a DNA readers.
Meanwhile, the other two robots X-ray the humanoid. Nothing. Even at maximum power, the beams don't penetrate. Spectral analysis shows that the humanoid's surface contains both organic and inorganic elements, most notably silicon, aluminum, titanium, iron, copper, and others. A more efficient X-ray scan helps to get an image of the humanoid's structure.
Part 06
He is somehow a transformed person. The unknown material is mixed with human tissue. The brain is transformed and enlarged, stretched to almost half its length. Further, the material has permeated the spine, lungs, heart and flows through the blood vessels.
The humanoid is then transported to the ship in isolation for further observation.
Report from the Dragon2 team:
he's searched the prison on the Fury. Someone's been covering the tracks there, but some small samples have been found that have a similar composition to this unknown mass. But microscopic analysis shows no readable microstructure. On a molecular level, everything's disintegrated. The Dragon2 team may soon complete their exploration and head to LV-426
DNA analysis from the vehicle shows mostly DNA from two people, an android and an unknown human. No record. To a lesser extent, there are samples from two known individuals, colony personnel, the chief of supply and the second-in-command. To a lesser extent, there are samples from two other unknown persons.
Auntie reports that the drones have located a possible colonist site. A large lava tunnel in which empty cryo-chambers are visible. The position is approximately one kilometre from the edge of the anomaly. Second report: in the area around the anomaly, drones have detected more moving unknown creatures, four in total. Their danger to humans cannot be estimated.
The ship's sensors have completed a detailed scan of the vehicle. It appears there are explosive devices inside. They will continue to search the vehicle only remotely via robots.
Dragon1 is heading for the lava tunnel.
Part 07
They' re launching a small search drone. Inside the tunnel are cryo-chambers of various sizes, for humans and animals. Another part of the tunnel is covered in biomechanical material similar to an alien hive. Inside is a human person, presumably a woman, partially encased in a fibrous material like glue. It looks as if she has sat down in the tunnel and the biomechanical material has grown around her. Her legs, back and the back of her head are embedded in the material, her shoulders and chest look a bit bony. The drone hasn't detected any life signs.
After a few metres the hive ends with a mass of spider-like legs, they're half-cut facehuggers, maybe hundreds of them. Biomechanical roots are growing into them from the hive, as if to suck the nutrients out of them. Beyond that, it's just an empty tunnel.
Face analysis shows that the person in the tunnel should have been dead for over six years. She died on Earth.
Suspicions are growing that someone on this planet has been conducting illegal experiments on animals and humans bought on the black market.
Part 08
Time to interrogate the android. His name is Cosimo. He starts a conversation about how androids have no human rights. Otherwise, he says nothing at all. He answers most questions with silence.
Part 09
The Dragon1 team conducts a detailed and in-depth scan of the anomaly.
There are fragments of missiles in the surrounding area, probably the result of bombardments that the Colonial Marines can conduct from orbit.
It appears that the objects of the anomaly are slowly, at a speed imperceptible to humans, changing shape and moving towards a single point, presumably the original position of the unknown object that was there before it was shattered by the blasts.
Depth scan:
Below the surface are a number of long and richly branching tunnels extending to depths of up to 900 metres. There are also structures resembling roots that extend to depths of over 5 kilometres. In the centre of the system at a depth of 500 to 700 metres is a smaller system of tunnels and chambers that resemble the internal structure of termite mounds or anthills. The entire underground system comes to the surface at a point that coincides with the original position of the destroyed unknown object.
Crew member Ron voices his speculation, "They're aliens! Even when we first saw this thing, it was clear it wasn't some kind of experiment. And now that we can see beneath the surface that the thing up there is just the tip of the iceberg, this simply wasn't created by any human or android, these are aliens."
The others are skeptical, never on any planet have more than primitive sea bugs been found.
Auntie is unable to analyze the situation. She recommends they withdraw and await orders from command.
Some team members are leaning towards the possibility of exploring the tunnel in person. After the robots rule out the presence of planted explosives and other hazards.
Team members Tess, Alice, and Ron volunteer for the exploration.
The captain decides that two humans are enough and will be guarded by 4 robots for sure. Tess and Alice are going down.
End of short version.