4. What Went Wrong?
So we know by what happens to the decapitated Engineer's head and that the Engineers got infected. We also know that the pile of dead Engineers have "explosions from the inside" of their heads, so there certainly seems to have been an outbreak. So at some point at the brink of sending out the Juggernaut to Earth (again we see the preparation take place in the David scene with the holograms on the main control deck) this outbreak went crazy. Engineers were either on all out attack trying to get to anyone that wasn't infected or simply went nuts and died from their infection. The question is did the lone surviving Engineer in the hibernation pod unleash the virus (making him the Prometheus of the story and pissing off the Gods) or was he just laid out ready to take flight on the mission and just missed the outbreak by blind luck? He seems to want to carry out Mission: Take Out Earth the moment he wakes up anyway so this all seems pretty cut and dry but potentially there's more to this. Who knows what David said to him? Up until that little speech he didn't seem too evil. Or maybe just having the realisation the Human scummers found LV-223 on their own accelerated his desire to shut them down.