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: 
Self Replicating Drones

The enemy race drops a 3d printer/mobile factory on an asteroid. It starts building more of itself, and creates swarms of drones. It keeps doing this. Eventually there are so many drones you can't have a civilization anymore, either because enough of the mass of the solar system is converted into drones, or you give up and leave and the factories go into hibernation mode.
I'm going to take a simplistic shot at this, forgive me if I don't 'color inside the lines'. In the OP "uninhabitable" and "diaspora" made me think that a civilization capable of such destruction would also likely have no issues with Biological weapons.  

 In the basic premise of the pathogen seen in films like "Alien: Covenant", I suggest that a universally lethal-to-all virus/prion or other pathogen would fit the job.  

As a self-replicating, incurable weapon...deploy once, then step back and wait.