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The alien ship appears to be stranded and inoperable for the 20 years it hangs over Johannesburg. Early on we are shown that a small vessel had detached from the ship and disappeared.

Approaching the movie's climax we learn:

1. The small vessel was hidden under a shack in District 9 the entire time.
2. The vessel is a command module that can activate the alien technology and the stranded ship itself.
3. Alien Christopher Johnson (and cohorts) spent 20 years collecting enough "fluid" from alien scrap metal to power up the command module ... and (he suggests) to subsequently get the entire ship very quickly to retrieve alien help.

All of the "fluid" needed to power the ship to leave Earth came with the ship itself. In fact, enough could be extracted just from the small pieces of debris that fell off of the ship onto the ground while it was stranded.

Even if we accept that the ship lost or ran out of the distilled fluid fuel, is there a good explanation for why Christopher Johnson didn't stay on the ship and extract it there directly, rather than going to the ground to scavenge it from scraps and distill it in a shack over the course of 20 years?

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    Your assumptions are wrong. The ship stopped on earth because of a likely leadership crisis, its unknown if christopher came with the control ship or it was ejected by someone else or automatically, only that christopher has it later and required fuel. The Aliens were more or less ‚forcefully‘ removed and relocated in camps. Access to the alien technology is alien genetic, so the rest of the ship and its resources were not human accessible and the reason for the movies second plot. – morbo Nov 4 '19 at 12:48
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    @morbo: the suggestion in your comment that every alien was forcibly removed from the ship could answer the question. I.e., if it was impossible for Christopher to stay on the ship, or to get back onto it, then that would explain why he had to resort to scavenging for fluid on the ground. But I did not see any suggestions in the movie that they forced every prawn off the ship, or that the ship was blocked after the rescue operation. (In fact, the ongoing appearance of alien weapons might suggest ongoing access to the ship.) – feetwet Nov 4 '19 at 18:12
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    I expect all the prawns were removed as there was likely no food there anymore...I suspect,like you,there was regular access to the ship by MNU, but no access was allowed by the prawns. – morbo Nov 4 '19 at 18:16
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As mentioned by Morbo in the comments, the ship stopped due to a leadership crisis, as prawns work as a hive mind and left with no leader.

Even the director explained the same thing, from io9

The hive mind [concept] is the most important thing to me, because I love the idea of a civilization that can build all of that technology and then, at the same time, just have a massive population that was just drones that needed direction, and were absolutely incapable of building that stuff on their own. I found that to be a really interesting concept. Also, it sort of explains why they don't turn on the humans. Individually, they may be feeling oppressed, but they don't have it together enough to form a resistance and back one another. So I found that really interesting.

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 breaks.

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