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The movie shows the majority of the aliens as unintelligent and seemingly incapable of operating, let alone inventing, a space ship. However, the exosuit/mech was clearly created in their image, weapons are hardcoded to work only with their DNA, and Christopher seems to know exactly how to operate the mother-ship and where their planet is located.
Why then were conditions inside the ship so terrible and why did it stop to hover above Earth?

All that seemed to be required to start the ship again was the black fluid that Christopher, his friend, and his son collect. They obtain this from various pieces of alien technology scattered throughout the slums. Of course this technology must have been located inside the ship, so why didn't they simply collect it during the few weeks between the ship's arrival and the hull being cut open by humans? It took them years to collect this small amount, but I imagine it would have been much easier to locate on the ship, and the process would have been much quicker with the other prawns' assistance.

If help was what they hoped to gain on Earth, why didn't they send an emissary instead of just letting the ship hover over Johannesburg? Clearly, it would have been possible since we see the smaller ship detach from the mother-ship.

marked as duplicate by Valorum, user1027 Jan 29 '15 at 1:07

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This was explained in an io9 interview with the Director, Neill Blomkamp. In short, the prawns are a hive species. When their leaders died, they became rudderless (and not a bit stupid and docile). In the absence of command input and realising that supplies were running short, the ship auto-navigated them to the nearest habitable planet to allow them to disembark and perform repairs. Unfortunately, they encountered us.

As to why it took them 20+ years to gather the fluid to fuel the pod, it seems that it took that long for a potential new leader (Christopher) to fully mature and start making intelligent plans on behalf of the hive:

What is your own back story for these aliens? What's their home planet like? Why did the end up on Earth?

The other thing is that the ship was meant to clip together with other ships. So there's, like, vast amounts of resources that they're bringing to the parent planet. And the ship, when the army generals or the queen of that particular ship died off by some sort of virus or bacteria that they picked up on some other planet, that killed them off. And it didn't effect these sort of resilient, hardy sort of drone workers. Then the technology is usually the thing that they relied on to save them, but in this case it sort of screwed them because it brought them to a planet that kind of treated them pretty badly, but it was the ship that realized that, unless it gets to a life sustaining planet everything is going to die, which is a cool idea. So the ship just auto-pilots to the closest one in the Goldilocks band, and it's our planet and then pulls up and hits the brakes.

Where does this leave Christopher Johnson [an abnormally smart prawn who sparks a bit of a revolution... Not to give too much away]?

I think it's taken 20 years. I think because there is a subconscious hive mind happening, really what they should do is lay one egg that has a different embryo in it that grows into a Queen or being someone that dictates direction. But I think in the interim, because they may have done that, there may be an egg out there with that, but as that being is growing, I just like the idea that he may have been a lot more directionless in the beginning. But the hive structure of their society may just pick one or two that starts to become the leader. Like the overall structure of his brain may change because the hive may want that to happen. So he starts having a direction and a goal. Which is an interesting idea and it's just enough to kick start them to be able to get to the ship to get back.

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