I can see a sequel working despite the fact I had a ton of issues with Prometheus. This would be my ideal set-up for a sequel:-
Shaw and David make their way towards the home planet of the jockeys. Along the way, Shaw finds out that David was asked by Wayland to infect Charlie. David appears remorseful of this but tries to defend his actions. Shaw discovers that Wayland had planned on testing the black goo on a human first before using it on himself in case this was the building block to immortality. However, once he realised the goo caused mutations, he realised the answer lay elsewhere. Shaw and David enter the planet of the Jockeys and quickly see that Engineers have been creating humans to use as slaves to build their opulent planet and to also study how advanced they become. (This will allow a bigger Human cast to feature). Shaw and David discover a small band of humans who have been trying to find out their purpose for existence and can't quite relate to Shaw as they're not from earth and have no real connection. Shaw explains that the engineers have created earth, a planet full of humans, with families, friends, etc and it is the Engineers game plan to end their lifecycle so they can start over again. The humans wish to visit Earth and to experience what Shaw has.
In a unique twist - Meredith Vickers - had managed to send a distress signal back to Earth during the events of Prometheus, leading to Weyland-Yutani sending a group of mercs to investigate. They pick up on a signal from David in space and follow the jockey ship. Both vessels land and Shaw and the mercs investigate the jockey home planet. Shaw tells them that the engineers are to be studied and not destroyed. The mercs state they are on a mission to bring back specimens. Shaw states that nothing they create must enter Earth.
The engineers plan on launching a full assault on Earth as the final jockey from Prometheus sent a warning to them that their goal had been discovered by humans. Jockey soldiers manage to capture Shaw and David. David explains that they simply want to know more about them but Shaw wants to understand why they wish to destroy us. Shaw tells David to explain to the council of Elders that they will fail in their plan as Earth will fight and destroy each and every one of them and end their plans. This enrages the Elder Jockeys - these will be monstrous versions of the Jockeys in Prometheus. The Elder Jockey then begins to unleash the true Xenomorph onto the planet in an attempt for the beasts to destroy the crerated humans but they fail to realise that these beasts cannot be controlled or stopped. Many xenos kills humans as well as hundreds of Jockeys. Shaw, David and a small band of humans make for a desperate attempt to flee the planet in one of the jockey ships. On board, a huge Elder jockey engages in a fire fight with Shaw and a few humans. David tries desperately to set a course for the ship to flee too but he doesn't quite manage it before he is torn apart by the elder Jockey. Shaw and the small group of humans attempt to regain control of the ship whilst fighting off xenomorphs, Shaw and two of the humans are hurt. The rest of the humans are destroyed by xenomorphs. The elder Jockey returns to the cockpit but Shaw has managed to lock him in with a Queen Xenomorph who had been previously kept in the cargo hold along with thousands of eggs and would also be unleashed on Earth. The huge Jockey and queen fight but the queen manages to impregnate the main jockey before he manages to kill it by crushing it and firing it out of a portal. Shaw and the surviving humans escape in a small alien vessel. The jockey manages to sent a warning to the rest of his race before succumbing to a chestburster. The ship crashes on LV426. Fades to black.
