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I got this really interesting setting where Humanity is reduced to a few shattered outposts in hiding and a community that has fled to take refugee into an isolationist alien empire. But I'm having trouble figuring out a believable reason as of how it ended up this way.

My initial idea was that Humanity was attacked and almost wiped out by some rampaging insectoid hive mind (like Rachni or starship trooper bugs) but that explanation just clashes with the larger galactic community setting. I want a huge amount of races living under a sort of unified galactic government. This society can't have taken in Human refugees, and need to be in peace/alliance with whatever wiped Humanity out. They would also be generally unaware about the existance of Humanity 200 years after the destruction, so it wouldn't have been a major event for them.

There are a lot of races, and Humans would've been a pretty new one when the destruction happened. That helps somewhat in making it not a big deal. And the story will be about secretly striking at whatever tried to wipe us out.

But what could have almost wiped us out in the first place? And stopped all but one isolationist empire from taking in refugees?

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  • $\begingroup$ "I got this really interesting setting where Humanity is reduced to a few shattered outposts in hiding " - no man, no, it's not :). Do as usual they nuked themselves, and those who are left were just forgotten and not interesting for anyone, or out of reach. $\endgroup$ – MolbOrg Jun 13 '17 at 2:27
  • $\begingroup$ Have you read the Uplift series by chance? Just because the races are collectively in agreement about certain things doesn't mean there isn't still war. $\endgroup$ – Draco18s Jun 13 '17 at 15:28
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/And stopped all but one isolationist empire from taking in refugees?/

You can back into it from this. Why refuse refugees? Because they are sick and you might get sick too. You can have humanity perish because of some contagion - something which could also possibly affect the other spacefaring races.

You need to make your isolationist race different somehow such that they take in humans despite the risk of contagion. You could make them so different that they are not worried about any human disease - silicon xorn or something. Better, though, would for them to be very much like humans (or perhaps they are humans, from the paleolithic human diaspora) and not care because they don't care - a mindset so different that the risk is not something that preoccupies or even occurs to them. You can have fun writing characters from this empire.

The question remains: what is the contagion? How does it work? How is it transmitted? Is it really transmitted? Is there someone or something responsible? There is your story.

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    $\begingroup$ I quite like this explanation, however it doesn't quite give a reason why Humanity would still be hiden after 200 years. So I think I'll expand on it by saying: the dissease was caused by one of the elder races of the community who deemed Humans too aggressive. This race would have a long history of these pre-emptive strikes and so the rest of the community just kind of falls in line and stands by while it happens. This cause for the dissease gives me the enemy I need to fight against in the story. $\endgroup$ – Wissieze Jun 12 '17 at 7:15
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    $\begingroup$ An biological infection that could cross between independiently evolved life beings would break my suspension of disbelief into pieces smaller than a virus. You can resort to a gray goo, but then the isolationist empire has no reasons to think they're inmune. $\endgroup$ – Rekesoft Jun 12 '17 at 9:26
  • $\begingroup$ @Rekesoft - why do you assume a biological infection? Why do you assume the isolationists think they are immune? Free your mind! $\endgroup$ – Willk Jun 13 '17 at 18:06
  • $\begingroup$ @Will What kind of non-biological sickness which causes massive contagion were you thinking of? Homesickness? Nostalgia? $\endgroup$ – Rekesoft Jun 14 '17 at 7:13
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I really like the approach & answer of Will, but there are also one or two other (through possibly problematic) options.

From how I understand the description of your galactic community, they are a generally peaceful bunch, that don't normally allow members to wipe out other (sentient?) civilisations. There's only two ways to go around such a regulation:

1) Humanity was not legally protected by the laws of the galactic community. This might be due to some loophole affecting only the once species which attacked humanity (see below for ideas), or maybe humanity was classified as a 'dangerous/not peaceful' civilisation (think global warming, wars between human groups) and that one member of the galactic community took immediate action - maybe not even informing the other races.

Reasons why one species might have a reason (& a loophole) to attack humanity could include:

  • disease - they are prone to die from contact with humans are are somehow allowed to take preventive action
  • territory - they can claim our solar system as their rightful territory, which humanity 'invaded'

2) Without legal coverage the 'aggressive' race will need at least as strong motivations to attack (the ideas are still the same though). In addition they will not cover up their breach of galactic law - maybe just with a quick attack on humanity and not telling anyone about it. But if human refugees could reach other races, that would be bad for the, so they'll need to prevent humans from being accepted as refugees (either by not letting them arrive in the first place, or by diplomatic means).

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  • $\begingroup$ I think I'm going with a combination of your and @will his answer. The contagion would have been caused by one of the leading races in the galactic community. And they use their massive influence to intimidate everyone from taking in the Humans. $\endgroup$ – Wissieze Jun 12 '17 at 7:18
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I like the idea of a contagion, but in a spacefaring society quarantine is not difficult. The 'infection' needs to be able to overcome disease quarantine measures, present a credible threat two hundred years later, and give species with completely different biology a reason to reject survivors. I can immediately think of two solutions, both variations on the same theme.

Malevolent AI

An intelligent AI, or group of them, decides for whatever reason that it's going to exterminate humanity. AI are smart, adaptable, and single-minded, leaping from network to network and killing as they go. Other civilizations take advantage of the situation by allying with the AI over the remaining humans. The survivors are the only people remote enough to stay beyond the AI's reach, and stay disconnected. Any contact with leftover human technology would spell certain death.

Singularity

Humanity changes into a new form- maybe it's a hive mind, maybe it's merging with AI, maybe just old-fashioned cyborgs. Whatever the root cause, this new force is determined to assimilate the rest of humanity by force. Other races, not wanting to get on the bad side of the 'legitimate' human government, refuse to take in refugees and leave the survivors to fend for themselves. The survivors go into hiding.

I'm sure you can come up with a variation on this theme that will work for your story. By having something 'usurp' baseline humanity and become recognized as the new 'legitimate' government, you have your threat, a reason why other species wouldn't take refugees, and a justification for the threat persisting, all in one.

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The isolationists are the cause.

Known, or unknown, to Humanity, this fits everything. They're not part of the galactic Union, but not necessarily at war with them, as they're isolationists. They could be geographically close to Humanity, thus the first peoples that Humanity ran across.

It doesn't even have to be intentional. What @Will mentioned with a contagion could work - Something this isolationist species carries naturally happens to be super-contagious to Humanity, and only people with a specific gene sequence aren't affected by it.

Or, perhaps, it's a different sect of these isolationists, and the Isolationists are using Humanity as a weapon to strike out at them. The Galactic community doesn't necessarily know of, or care about, Humanity so their response to Humanity doing things is going to be different. Humanity could even be in on this deal, being funded and equipped by the isolationists to go fight their common enemies.

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Absolutely believable reason? Only a tiny fraction of the human population could go to space¹ still fewer could reproduce an environment that let them survive in the long term. Meanwhile global warming continued unchecked on Earth, reached a tipping point, and wiped out Earthbound humans along with most other higher life forms².

¹Consider the tiny fraction of the population that ever went on ocean-going ships.

²See Permian-Triassic extinction.

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Humanity have just collapsed itself.

This fits with your criterion that the 'cause' must be at peace/ally with the Union.

Human is not a peaceful race. It has waged war among the members of their race themselves. What could be more logical that the greed has devoured each other countries in a black hole war?

Or, under the weight of their technological advancement, human have just been swallowed by an experimental technology failure (attempt of FTL collapsed the whole solar system).

And these are not new. Many galactic civilizations have succumbed to either of these, and the Union just regarded this as a natural selection, thus refusing to intervene in taking in the refugees.

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