The original script varied quite a lot from what we finally saw, but a lot of the material wasn’t re-shot, so we ended up with a mess.
In the original script, the Engineer had been infected by “something”, possibly the black tar, possibly something connected with it, possibly something the tar was supposed to counteract. To save his life, his crew had placed him into suspended animation. Then his crew got slaughtered.
When Weyland woke him up, it was a death sentence. His ship wasn’t working. he had no one around to treat his infection, and he couldn’t go back into suspended animation.
That did not make him happy.
Then he realised that the humans either had been infected by the same thing that had infected him. So he set out to destroy them all so that they couldn’t spread the infection. When he discovers that some humans had escaped in another spaceship earlier, he sets out to sterilise the Earth. The humans stop him, and leave on another spaceship.
The Alien was supposed to be the last thing that survived on the planet, emerging from the Engineer, who staggers to his chair and sets of the warning beacon. We then see the alien laying eggs in the hold after the heroes have escaped assuming nothing remains.
With rewrites it all became nonsensical. Instead of the planet just being a jumping off point for an extended universe, it was re-written so that Weyland knew about the planet, even though 100 years its existence is unknown. So the planet looks exactly the same, the ship looks exactly the same and has crashed the same way, it is connected to the Aliens, but it is canonically not the same planet. The Engineer attacks, but for no reason, and then sets out to destroy the Earth, even though that’s obviously pointless since humans have spaceflight and have already spread throughout the universe.
The whole thing is an incomprehensible mess, but the original script was much more coherent and actually pretty good from what I’ve seen of it. It tries to explore issues of what it is that separates Gods,Men and Monsters and the distinction between creator, mother and host. It also throws in some interesting abortion/infanticide analogies by looking at whether an individual can justifiably terminate an unwanted lifeform, and whether that changes if the lifeform is intelligent or is just capable of becoming intelligent. You can still see hints of some of those elements in there, and the phallic symbolism of some of the monsters and sets makes a lot more sense with that as the subtext.
But the rewrites just produced a mess.