Breeding grounds?

The black goo was pretty obviously dangerous, there were holograms of them mapping their way to earth, and the ship is STOCK piled full of the black goo urns it definitely seems like they had malicious intents.

Yeah, me neither. I was skeptical about any analysis offered by the human characters that had no prior basis. The military complex comment came from the captain, and I took it as he's basing his assumption off of his personal, perhaps military experience. Essentially, he's a soldier, so he sees a military complex. Just as the scientists see a tomb or whatever. The only one I MIGHT trust would be David, but he doesn't really speak on the matter that I can remember. I'm not sure I agree on the xeno breeding ground idea. If the engineers were servants to them, I would expect them to already exist or be represented some where in the facility. For instance, a large xeno statue, rather than a huge engineer head (or whatever that's supposed to be). Personally, I believe that the xenos will eventually emerge through evolution as a part of the black goo effect, whether that's through the thing we see emerge from the engineer corpse at the end, or something else. I would say based on the creatures we saw in the movie, we have a long way to go till we get to the xenos we know and love. Just my opinion, though.

They make the conclusion very clear, and the reality is something that's been referenced in many alien films. Janek makes the conclusion [i]for[/i] the audience. The black goo is a weapon, as are the Xenos. Simple, easy, makes sense.