The machines from the Revelation Space universe bent on the supression of intelligent life are transported to the ST universe by some Federation researchers by accident. The said researchers activate the machines, and get converted into usable mass for the machines replication for the troubles
The machines have examples & all the knowlage the researchers & the computers had and thus can reverse engineer Startrek technology
The said machines from Revelation Space can effectively turn 'off'(or tone down) the laws of Interia with ease. Against an active star faring population, the machines can deploy a collective mind for selfmanagement.
The machines have a massive library of ways to kill various active intelligent races. Including, but not limited to, 13 different ways to kill as star. They have demostarted the ability to deconstruct gas giants & other planets for raw mass in a matter of months. Energy is a non-issue(they use ZPE), but they dont have an effective energy-to-matter conversion system.
The machines can deploy nanites, that can in a space of minutes, breach a ship harded against nanites, construct an machine-human interface into the 2 humans on board(with no prior knowledge of what a human is), extract every thing the people knew, make a bunch of decisions & withdraw completely from the ship & said humans with no side effects.
Weapons that have been used against them(unsucessfully), are weapons which can quite handly smash planets to atoms. A single ship armed with a dozen or so deployed them against the machines. The said weapons can move independantly of the ship that deployed them, they didnt last very long.
However, they do not use FTL anything! The reason for this is the prohibitive side effect of FTL travel. An example of why:
An example is when 2 techs are operating the FTL thingy, only 1 comes out. And everyone thinks the said person is mad cos they insist that there was another person there as well, instead of just 1 person
In the last book, we find out that entire civs have been edited out of history. A truely scary temperal weapon of mass destruction on a universal scale.