So Prometheus is the movie title, also the name of the ship in the film .. we know that already. But lets pretend its also a lose easter egg thats been hinting at the plot the entire time? So "Prometheus" isn't a person in the movie, its the crew acting as the role of Prometheus in Greek mythology. Humans were created long ago by the Space Jockeys and we are their children.. they are by definition our gods. The Space Jockeys uncover humanity's wily intelligence, in that we have ventured into space and found them. The crew (Prometheus) steals their fire (bio tech), and the Space Jockey's (Zeus) unleash their Xenomorph (Bird) to punish them.
From here the Prometheus script does what it pleases, and some turn of events allows the wily humans to turn the xenomorph against Space Jockeys and barely escape. We see the Space Jockey ship in the Prometheus trailer, and we see something crash. Prometheus and Alien are tied together via the Space Jockey ship, and loose ties to xenomorph introduced late in the film. Somehow a Space Jockey gets impregnated by a face hugger and after coming to, decides to unleash its wrath on Earth. The movie is taking place at LV426 at this point. The humans are on the planet, the Space Jocket flee's to the ship, takes off.. gets nearly in orbit when the chest burster scene happens. The ship comes crashing back towards to LV426. The humans have survived, they escaped the SJ and its xenomorph pets.
Lastly there are some hints that the chest burster from the Space Jockey is the queen who later lays eggs on the crashed ship for the crew in Alien and colonists in Aliens later find. Her size and intelligence (to use an elevator for example) is explained by her mixed DNA with a Space Jockey. The movie ends with a panned camera angle of the crashed ship, even further out to LV426 and lastly harrowing .. pronounced and familiar beeping a warning beacon earlier activated by one of the humans on the ship. End
That of course leads right into the Nostromo picking up the warning beacon some 50 years later at the beginning on Alien.