I would like to sit down with Ridley and the writers of Prometheus 2. They set up SO much stuff that can be held dormant until Alien 5, which I would bridge together.
Let's say David and Shaw set autopilot on the new ship to the home world of the Engineers. It's in a solar system where two planets in the system could sustain life and are similar to earth. One of those, though, has been abused for testing (as Janek predicted) and has become a sphere of failed experiments, chaos, and takeover from an entirely new breed of creatures. The Engineers won't dare set foot down there. Since the ship that Shaw is piloting hasn't been updated with this info, it returns to the planet.
David tells Shaw not to go outside because of his readings but she decides to leave anyway. It's tropical, breathable, and there is a large formation in the clearing similar in design to a space station, but on the surface of the planet and made primarily of rock. Shaw and headless David enter and discover it's a facility the Engineers were using to create and/or clone humans.
They find a room containing maps and schematics, and David finds tools to reattach his head. In what seems to be a large lab-esque room, disfigured humans are contained in a number of stasis tubes. They bring one down to open it up and out comes a disfigured woman with tubes spliced into her back and arms. When she wakes, Shaw believes she originated from earth over a thousand years ago and was abducted and experimented on. Opening that tube sent a signal to the functioning sister planet and the Engineers send a probe to the test planet to see what's going on. While Shaw, David, and the earth girl are making their way back to the ship, a probe ship enters the area and organically mutates into attack mode. Suddenly, it gets attacked by flying xenomorph creatures and gets taken down, pulled apart, and eaten. The three race back to the ship.
Shaw wants to leave the planet, but David insists they're in danger. It is uncertain (again) if David has other intentions...
David's schematics pulled from the cloning facility indicate there is a transport station on the other side of the planet that has a vessel so small that it can escape without being detected. David pilots the ship (which is now being attacked by creatures from the outside) and heads for the transport station. When the hull starts breaking away, everything suddenly stops harassing them and they are smooth sailing. This is because the xenomorphs from the outside are realizing they're outside of their own territory. The ship is damaged and David can't fly it all the way there. They land near a wreckage.
David leaves to observe on his own while Shaw studies the earth girl and places her in a stasis chamber. Outside, he explores the wreckage and finds an Engineer trapped under debris and barely alive. He utilizes a seesaw method to free him. David communicates with him and explains that they have commandeered a ship nearby and want to go to Earth. The Engineer explains his crew betrayed and left him there to die and points to the footsteps in the mud. David and the Engineer return to the ship, though after they leave the wreckage, we are shown a dragonfly-esque alien species with a large egg sac landing on a low-hanging tree branch.
Shaw wants to bring everyone back to Earth. The Engineer opens a holographic panel, makes some changes, and the ship is back online functioning in a secondary mode. It's an uplifting, happy moment for Shaw and David until David realizes they're heading to the Engineer's home planet. Shaw removes the pilot helmet from the Engineer and stabs him with a pipe that broke inside the ship's interior. David has no choice but to land on the home world, yet the ship they're flying has a hive of dragonfly xenomorph attached to the hull...