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Instead of some attack that defeats the human, rely upon human failings and create an Arms dealer that wants something common from their side but not common on our side. Rare earth metals, rare compounds only created by asteroid collisions, first edition OSR books, etc. As for the difficulty of reverse engineering technology. It is pretty hard the less advanced you are to the culture that created it. Consider that the Romans had the material science needed to make many WWII weapons, but not enough other science to pull it off.
@Flotolk, you aren't far off, but IR signature and stealth in space is one of those things just can't be beat without magic. You can observe an object and tell if it is too hot or two cold with technology we have today. A really large asteroid with a really small habitat in it might have a small enough variance that it is written off as error, after the first observation. Subsequent observations, though, will improve the odds of detection.
@flotolk, so maybe. However, we are talking space, with a background temperature of about 3 kelvin. The normal idea of a "heatshield" is something that absorbs heat safely, and radiates it safely, usually as photons. So, your heat shield will glow in IR, just as well as the asteroid does, against the near perfect cold of space.
It is related to gravity as well. Gravity curves space-time. You aren't going anywhere on the surface of a heavy star, but time is warped. Outside the presence of gravity, where space-time has no warping, you get a similar effect. Though I think I got it backwards. Time outside of your anti-gravity zone is frozen. If you spend an hour in there, when you return, it is the same time as when you entered. So you could go in wounded, heal up, and come out and it looks like super healing.
Just thought of something else. In a very large rock, if you go deep enough and the life support is for just a few people, then the heat radiation will propagate at a certain rate through the rock, but it would take some time to heat the entire thing to the point that it's noticeable. Which implies there is a safe time period one could inhabit this hiding spot. The bigger the rock, the longer the time.
Good point @Jim2B. However, we miss asteroids because they don't have internal heat, just absorbed heat from the Sun so they are a bit cooler. Also, we don't have a 360 degree scanning regime at the moment, which goes back to your original point if we knew where to look. I expect we will have constant scans in the future, though.
You can't hide the thermal signature. Keeping it warm enough on the inside is going to make it warm on the outside. Viewed in the right spectrum, it will shine. Same for the ship heading there. With current technology we can see an idle Space Shuttle with life support going if it was orbiting Saturn. It's heat signature is unmistakable. The temperature above background makes it easy. The best way to hide is it this way is to create a hole in whatever sensor nets normally look in the right wavelengths. A random ship might scan there, but thats the risk.