Question: For the Universe I am creating humanity has devolved into groups of scattered tribes. This is due to the fact that we ran afoul of a *really* nasty alien race, who decided to leave us homeless. A coalition of races had banded together to fight this menace, but mankind ended up with the short end of the stick. It is the Great *Diaspora*, and we are only hanging on by our fingernails.

The problem I am having is how to thoroughly destroy or at the very least render uninhabitable the places Man once called home. If it were only Earth it would be a simple enough matter, but by the time the attack takes place he *also* has colonies on Luna, Mars, Ceres, Callisto, and Titan. How can I muck them up badly enough that we have to now seek a Promised Land elsewhere?

Ceres I figure is small enough it could just be reduced to rubble, but what about Luna? If you destroy the colony there, what would prevent them from setting up new ones a few hundred miles away? 

At the moment all I can think of is a "Gray Goo" weapon, short of blasting multiple planets and moons to smithereens. I am hoping there is another option out there I haven't considered.

EDIT: I'd like to hold onto the Sun. You know, sentimental reasons. :)

Answer: 
So, to take a stab at this, destabilization of the oort cloud, millions upon billions of icy debris, with a vast number of objects over the size of 1km. A dead star swinging by the very edge of our system could easily dislodge of a few billion kilometer long pieces of ice. Just for good measure there could be ancient dormant prions, as mentioned in a previous post, that inhabit them. Fast forward a bit and you literally have an entire solar system getting pelted nonstop by large glaciers filled with deadly viruses/bacteria, or whatever you want them to be, quickly causing the entire solar system to go to shit.

This would take care of pretty much any base that's not heavily armored, even if it is, just chuck a few hundred abnormally large iceballs at it.

Lastly, for the long term, instead of rebuilding, just say that with the billions of asteroids that are being swept up, it'll be a few hundred years before its cleaned up enough to not have to worry about being on the surface of a planet. Either that or viruses.
Destabilise Pluto, setting off a series of disasters
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With a small change of orbit, Pluto can be made to viciously slingshot around Neptune. It hurtles towards the inner solar system and wrecks Earth.

In the meantime, Neptune's orbit now brings it into collision with Uranus and eventually Saturn and Jupiter. The Solar System is now the Solar Splat, and mankind can't even decide if it began with the aliens altering the orbit of a planet or not.

Depending on the details, mankind gets weeks or a few years to get out of the area as Earth and the colonies are destroyed in sequence.