So, it's several hundred years in the future and the majority of humanity now live on artificial habitats, either clustered together into nation-sized groups or scattered individually across the solar system. Technology has advanced pretty far, and while we haven't figured out stuff like Alcubierre drives or artificial gravity; we do have reliable, powerful, fusion for ship drives capable of efficiently giving a ship several hundred km/s of delta-v.
Out of the depths of space comes an automated alien ship. It has spent centuries traveling from another star a hundred light years away; sent by a race of aliens that had just been taken over by their own version of the Third Reich when their astronomers reported that a little planet a hundred light years away had the perfect conditions for life. Being completely reasonable beings, they decided the most logical thing to do would be to send a ship to make sure that whatever is living on that planet never has the opportunity to develop into something that can threaten them.
So, it's a single automated alien warship vs. the collective military might of somewhere around 20-30 billion humans, most of whom live in space. The human ships are armed with kinetic kill missiles capable of hitting with the energy of a tactical nuke, cannon capable of firing heavy projectiles at several dozen km/s, Casaba howitzers, and lasers. For defense, they have defense grids of railguns, lasers and particle cannons for vaporizing incoming projectiles, as well as powerful magnetic shields for protection against radiation, particle beam weapons, and the vaporized debris from incoming projectiles. They have engines that use some undefined method of fusion to provide several hundred kilometers of delta-v at a fairly sedate acceleration, or throw themselves around at several g-s in an emergency. Pretty agile for something that masses over a hundred thousand tons.
This level of human technology is pretty impressive... in fact, it comes pretty close to the most advanced level of technology that we humans are capable of predicting within the bounds of hard science, and that's the problem. What technologies can I give the alien probe that would enable it to utterly outclass the human fleets, while remaining within the bounds of hard science fiction?
EDIT: To be clear, in order to be a threat, this alien ship has to be capable of dispatching hundreds, if not thousands of warships like the ones I've described, and then still have the capability destroy every habitat scattered across the solar system, and THEN still be able to wipe Earth itself clean of life. About the only limitations I'm putting on it are: No future fantasy (hard light shields, warp drives), and an upper limit on size of somewhere around a billion metric tons.