Scott has promised that Prometheus 2 will answer many of the questions left open in the 2012 film. However, Scott has told German website FilmFutter (via bloody-disgusting) that he won't show how the Prometheus franchise connects to Alien in the next film. He's saving that reveal for ... Prometheus 4?!
"It won’t be in the next one. It will be in the one after this one or maybe even a fourth film before we get back into the Alien franchise…," explained Scott. "The whole point of it is to explain the Alien franchise and to explain the how and why of the creation of the Alien itself. I always thought of the Alien as kind of a piece of bacterial warfare. I always thought that that original ship, which I call the Croissant, was a battleship, holding these biomechanoid creatures that were all about destruction."
Jon Spaihts' original script for Prometheus was a direct prequel to Alien. In it, David (Michael Fassbender) the android comes across and revives the Space Jockey (also referred to as The Pilot) who was last seen as a fossil in the 1979 film. We would've seen how The Pilot ended up dead on LV-426 from a Chestburster, but that storyline was jettisoned during extensive rewrites. Instead, Scott chose to have David and the rest of the crew end up on a whole other moon and come upon the Last Engineer.
Prometheus 2 will begin filming in February of 2016.