[NewChief]

I watched this last night and enjoyed it. Here's my theory:


The Engineer at the beginning is terraforming Earth. The problem is that the sacrificial drink that he uses to terraform earth is contaminated with the black mutagen (which he doesn't realize, hence his look of surprise when it works differently than he expected). The spaceship goes ahead and leaves because it doesn't realize that anything has gone awry.

Meanwhile, The Engineers back on the moon base have now realized there is a contamination outbreak that's out of control (thus the fleeing holograms and massive graves). The mutagen takes over the facility and corrupts all the "normal" material in the storage areas except for the ones in the actual ship (which are arranged differently and don't appear to have the leaking/condesnation issues).

The surviving engineers on the moon go into survival mode, trying to figure out if any of the contaminated mutagen had escaped the planet. The whole holographic scene where they're scanning the universe with 5 of them and find Earth shows them where it escaped to. What I don't understand is why they wouldn't launch an attack no Earth at this point. Maybe they're trying to clean up the contamination on the moon first? Anyway, moving on.

What this means is that humans are actually a result of the mutated/corrupted DNA (similar to an Alien). This is why the Engineer reacts so strongly to them when they wake him. It's not that he hates his creations, it's that humans are a corrupted version of that creation because we were created from a terrafarmer who accidentally used the mutated DNA to create us. I also like this because it explains humans resilience and destructive nature (after all, we end up beating the Aliens, right?). The mutagen just "weaponized" us differently and more subtly than the other creations.

Anyway, I read other explanations after I went to bed last night which also make sense, but I kind of like mine as an alternative way of looking at it.