You have to build colonies and spaceships and weapons to defend the colonies.
You are warned by an alien race not to send probes to Mars. If you do, you get attacked.
Your colonies are primarily built on the moons of the other planets.
Your goal is to build a huge space ark.
This sounds like Millennium 2.2, also known as Millennium:Return to Earth. I had it on the Atari ST, and remember sending probes, and the attacks if you send probes too far out.