One of the questions that got stuck on everyone's minds (including my own) after seeing prometheus was: How is the Deacon related to the xenomorph we know?
And it's true, it's quite a puzzle, that the creature left light years away from lv-426 is the cause for the Alien series. The other thing is the Hammerpede, and why it looks like the facehugger, but is a completely different beast altogether. Are they primitive forms of these creatures we know or are they just a lousy replacement in the attempts to recreate the fright of the original film.
First let us analyze the facts. And i'm only considering the original Alien films here, not comics, books or AVP-
The first thing to notice is that the xenomorph we know came from a ship. One that seemed to be left behind during an expedition or attack.That SINGLE ship was responsible for the events of Alien.
Now notice how it's only ONE ship. We know nothing about the other's cargo.
Then in Prometheus we have black goo. And another ship, this time armed with this viral component.
So, here is my suggestion: When the engineers seeded Earth. Their intention was to create humans, but for that to happen, thousands of other species (with similar characteristics were also affected), mammals, apes. From rats, to tigers to apes to us. We all share the same reproductive system and the same reproductive organs.
So, isn't it only logical that the same would happen with the xenomorph? Different species, same reproduction methods, different in appearance. Maybe the hammerpede is just another species that has a similar look to a facehugger. And the deacon is a different cousin to the xenomorph, like the orangutang and the lemur. Four legs, fur, climbs on trees, same internal organs....different species.
It's easy to imagine if the black goo was unleashed upon a planet, an entire ecosystem of these beings. Trilobites roaming the seas, xenomorphs sprawling from caves and deadly swamps full of hammerpedes. Different species, similar features.
Bottom line is: We don't even know what the other ships carried. BUt maybe it doesn't all lead to the xenomorph. Maybe he isn't in the center of this, but belongs in his own ecosystem, one created by the engineers.