Plot theory (lots of spoilers)

I saw the film last night and was a little confused, like many people about some of the plot elements. On my way home I suddenly realised what it is all about. This is my interpretation of the film. I know there are going to be some people that disagree, but it makes everything fit. If you disagree with this please come up with a better explanation which fits all the plot elements. - The Engineers are under control of the aliens, and in fact the Engineers may have been created by the aliens. The aliens need the Engineers to gestate which is why they don't just kill them outright; the aliens use the Engineers to mother their young and to perform engineering tasks like piloting ships (and probably building them too). It's no coincidence that the alien at the end kills the Engineer by injecting part of itself into the Engineer through the Engineer's mouth - just like the alien did in the first part of the film with the human (botanist guy wearing glasses) and indeed to John Hurt's character Kane in the first alien film. All of this shows that the aliens breed/control Engineers as incubators for their young. This is the key key point. Unfortunately the gestation results in death for the carrier, so the aliens need a fresh supply of humans. - The aliens (not the Engineers) are in control, they are the ones who seed life throughout the galaxy using the Engineers. What kind of life? Well, they need humanoid life to sustain their own, so that's what they seed first. At the beginning of the film we see an Engineer who has been dropped off onto Earth by one of those big round spaceships with his task ahead of him - he has to disperse his DNA thoughout the Earth to seed life, specifically humanoid life. He does this by drinking that wierd black stuff (the same stuff that David slipped in the doctor's drink?) - The archaeologists uncover the same star-pattern all over the world from ancient races and comment 'it's as if they wanted us to find them'. This part is not explained, i.e. how all these images ended up all over the world, i.e. how all these ancient races received these images, but perhaps Earth was visited by the Engineers when human life evolved. Anyway, the message is clear - the aliens (and their slave Engineers), definitely DID want the Earth humans to find them. - When the humans (after millions of years of evolution) travel across space and enter the control room of the alien spaceship and wake up the Engineers, then guess what? That's a signal that human life on earth has evolved to the point that it could then sustain alien life. In other words Earth is now ripe - brimming with billions of humans who can now be incubators for the aliens. The control panel lights up and the 3-d starmap shows Earth in red - Earth is now the next destination for the aliens' progress. - When entering the ship at the end of the film, David is asked by one of the crew what the place is they are entering and he says "It's a cargo hold". We are also told and see that there are thousands of pods. From previous frames in the film, it seems to suggest that the pods are full of little worm like creatures whose intermediate stage is the white snake in the black soup that got the biologist guy wearing glasses. If the pods are full of worms then that's probably enough to take over the whole of Earth. Whatever is in the pods, the message is clear - that the ship is full of alien life and it is headed towards Earth. - David says 'in order to create life you must destroy it first'. This simply means that most of human life on Earth is now going to perish when the aliens get there and colonise it, i.e. the aliens will flourish and multipy, the humans will die. The aliens' master plan is to use most of the population as 'incubators' and subjugate the remainder for the next stages. Not just on Earth but eventually all over the galaxy, all over their 3-d star map. - The confusion in the film, stems from the fact that the captain thinks that the Engineers created the aliens as some kind of weapon or biological experiment. If you turn this around, i.e. aliens creating (or at least controlling) pre-humans, it all makes sense. I think this is a deliberate attempt by the film writers to throw the audience and make the plot a little mysterious.