A civilization that can unwrap protons and build machines that violate energy conservation inside of them wouldn't need to care about taking over other species as basically all the material and energy of any solar system, regardless of whether it had life in it or not, would be available to them. And if you could build such objects you could probably find a better way to destroy our enemies than fiddling with their particle accelerators.

The Dark Forest idea is also very dumb. The universe is so stupidly big that going out of your way to destroy other lifeforms, especially if you are a technologically advanced species, is a huge waste of resources for no gain whatsoever. Furthermore, even in a hostile universe there is much to be gained from alliances, especially for intelligent lifeforms for whom the idea of a "civilization" is not tightly coupled to a specific biological underpinning.

I'm not saying a book couldn't be written with these premises. Obviously fiction can go all sorts of places. I just found the presentation of these ideas highly implausible in this text.