Well here's my theory, which I wrote on another thread but is extended here, though I should point out there's nothing really solid in the movie to suggest any of this, I still think some of it could happen since we really know so little about what really happened, but anyway here goes....
What if we only existed on Earth in the first place by chance, all because of this sacrifice engineer from some other cult, who acted against their Elders nearly 4 billion years ago, because they wanted to find out where they came from? In the course of time they discover their true origin, that they were once humans who would develop into engineers, so now we know what we are destined to become, why they visited us and would help us. Further to this, what if this cult didnt just create life on Earth, but they made this sacrifice to discover their origins in 5 other Earth-like places, hence the star map is created stating that human life existed elsewhere in the galaxy. When the Elders found out what this cult has done (4,000 years ago) they were very angry and begin creating a bio-weapon to remove all traces of their creations, and the reason is simple. They dont want the process to repeat itself again because it could threaten their own existance, they know what man is capable of through the ages because they had experimented long ago and decreed no one shall do it again. The cult is destroyed but all the Elders know about is the existance of the 6 planets. They sent out young soldiers to deploy this bio-weapon (the Hammerpede), created from another goo that gave life, also created by the Elders which the cult had stolen, and has now existed for 2000 years, the time it has taken for the Elders to extinqish man on 5 of the known planets and now we are the last. But before they can unleash this weapon upon Earth it gets loose on LV-223 and turns on the soldiers, forcing them to abandon their station.
As for what may have happened to those soldiers (engineers). My theory is it's the Hammerpede's that create the black goo, which contains 1000's more in microscopic form, and is stored in urns by the engineers to keep them under control. The engineers knew once the goo comes into contact with an atmosphere, those Hammerpedes would grow and spread quickly by attacking and laying their young inside the head of their victims, which would in turn feed off the brain before leaving by the mouth like the 'mother'. What the engineers didn't know, and where things 'could' have gone wrong, is with the goo itself which they thought was some kind of harmless preservative to sustan the Hammerpede's young. But when one of them escapes and an Engineer accidentally comes into contact with it, the goo unexpectedly developes into somethng else inside him. This is where the original xeno eventually comes from, and the whole incident is recorded as murals to warn others against tampering with it, both creatures are eventually captured and destroyed. What they dont realise until it's too late, is the same infected Engineer also came into contact with others. Further infection quickly spreads causing an outbreak and the soldiers are forced to abandon the waystation. Only a few Juggernaughts escape the massacre, and even then at least one of them is still carrying the infection. This ship manages to land on a nearby planatiod we later know as LV-426 and it's last occupant sends out a warning for all vessels to stay away, and the rest you could say is history.
