Actually, the opening scene tells us how the pathogen escaped.m That is, a "Good Engineer" discovered the plot to kill humanity on Earth, so he sacrificed himself to create a variant, likely the form of the original "Alien", and it was these mutants that killed off the other "Evil Engineers". Remember the noise just before the running holograms? That was the exact same scream as the Alien creature who had been born from corpse of the dead "Bad Engineer". The holograms were running away from several of these mutants. Remember, this is a prequil to Alien.
It's a pretty good theory, but this is mere speculation. But I do agree that we don't have a complete picture of the Engineer's ancient war against Humanity; it's not certain if it's the entire Engineer civilization that has enmity towards Humanity or if it's a branch faction that is at odds with us. Perhaps Ridley Scott would paint a more complete picture when he produces the sequel to Prometheus?
Think of the human virus as a biological terraforming tool we melt the ice caps desalinate the oceans causing more humidity cause co2 and atmospheric conditions to change to match the climate of the possible homeworld of the engineers if they built a machine with tectonics and civilization expansion there would have had to be a custodian think where and how in a thousand years what our verbal communication is likely to be given that Latin Aramaic incan Egyptian etc etc has become defunct obsolete how would you tell a generation in 10000 let alone 100000 years not to dig up the neuclear waste we are buring in Norway its one of the biggest debates on generational signposts at the min so as the engineers have done for thousands of years they seed worlds to transform there environmental conditions so when ams if they settle then the different conditions will he managable and they have genetically imprinted on our DNA to go find them so that's there alarm clock there were at least 4 other ships on LV223 do you think they will be empty I don't the goo is a evolutionary short cut it doesn't create life it stimulates evolution ie Fyfield no longer needed environment suit to help breathe i think they knew that we would eventually develop technological ability to find them hence the imprint of the higher being cave paintings with the only map to the outpost as a stepping-stone to become them evolve I also think they did the same with the predators home world but they rebelled that's they have been manipulating us to be more like them hunting us to eliminate the weakest of the strongest eugenics 101 that's why the predators invade alien infested worlds later to steal queens to gain an insurgents type of backwards engineering tech advancements
1 - Location of the Engineer's death. Possibly somewhere on Earth. My guess, the Victoria Falls in the Great Rift Valley, not too far from where the Lucy fossils were found.
2 - Circumstances. He's at the Falls, in his underwear, with his thermos of doom and a large ship in the background.
3 - Nature of Death, and the Properties of the Black Goo. Engineer takes the shot of goo, doubles over, and falls into the water as he's reduced to mutagenic sludge.
Engineer = Socrates.
Black Goo = Hemlock.
This guy may have been some sort of dissident or rebel. The powers in charge may have sentenced his to death, but allowed him to choose the means and location of his demise. Third rock from that star way out over there.
His remains, with all of the black goo's mutagenic abilities but without the malevolent aspects, gets into the water supply at the falls, is diluted and gets comsumed by some local primates, shortcutting the evolutionary process.
The rest of the Engineers don't pay too much attention to Earth. LV-223 is probably their equivalent of McMurdo Station in Antartica. Occasional expeditions may be sent out monitor things, and they're the ones who interact with the locals, telling them "Whatever you do, DO NOT GO HERE!", which Shaw and company misunderstand completely. (The cave painters are all from vanquished cultures which were mostly insular and isolationist.)
When the Engineers on 223 decide to exterminate Earth, it was probably because their projections showed that humans were becoming a real danger to them (or because they were afraid that their superiors would find out about us. After all, nobody thought anything of that what's his name who offed himself there eons ago, what's the worst that could happen. . .) Murphy shows up as they're preparing the mission, and everybody either dies or goes into hypersleep. Since the base is in the ass end of nowehere, and nobody else knows whats happening anyway, nobody checks up on them when they go offline.
Skip a couple of millenia, and have David wake up the rest of the passengers and crew of the USCSS Prometheus.
I suppose the evil engineers theorized that humanity was advancing at a high technological rate*Well take a look at the movie Prometheus.Humanity really made some good inventions along with the MedPod and space-faring ships*.And that one day humanity could surpass their technological advancements.I mean you wouldn't like someone achieving a higher position than you right?You gain some sort of a sinister plan to wipe them out so you'd still be the "Apex Predator".
So I think that the evil engineers manufactured the black liquid to eliminate humanity and erase a growing threat to the Engineers
Remember, according to the various works of fiction, the Engineers/Space Jockey's were adept at bio-engineering. The beginning scene of Prometheus could have been them performing an "experiment" to see what kind of life would emerge as a result of this.
Flash forward millions of years, humans have become the dominant life form on the planet. My guess is that an Engineer/Space Jockey ship scouting in the early first century A.D. took note of the large Classical Age Empires (Roman, Han etc) and figured that humans were sufficiently ""evolved" and "developed" enough for one last experiment-the Black Goo.
However, there was a containment breach and since they couldn't leave the facility either due to a lack of proper protective gear or something else, they decided to wait it out until the Goo dissipated or another ship came along.