According to Ridley Scott, Jesus was an Engineer sent to guide humanity back in the right direction after the they decided we were getting off track and becoming too warlike and cruel. We killed him, which is when they decided there was no hope left for us and that we had to be destroyed before we became a real threat.
The planned attack is ruined because of whatever extinction event involving the black goo getting out of control happens at that base, and when the Engineer wakes up, he finds humans who are just as petty (he sees them arguing and Shaw getting hit) as before, but now with enough technology to actually find him, trying to ask him for eternal life.
It's a
explanation, but sadly, it's the one he intended. Note that the film takes place on Christmas, so the 2,000 years ago thing refers to the death of Jesus.