Summary: Using self-replicating warships and mind uploading, a strategic mastermind is conquering the galaxy. However, they eventually run up against a truly challenging foe.
Their original identity was a subject of great debate in the eras that followed, if such an entity could even be traced to a single individual. They were believed to be an artificial general intelligence, an AGI, born by fusing transhuman super-geniuses into one entity. In the apex of their conquests, they were simply called the Subjugator, for the crushing defeats inflicted on all who stood against them.
The Subjugator was the first to make full effect of self-replicating weapons. With several safeguards against unauthorized reproduction, the Subjugator prevented craft from mutating out of control. In the rare event that such uncontrollable spawn did emerge, they were swiftly terminated. In this way, the Subjugator was able to establish the ideal weapons system for every theater. From combat nanoswarms for clearing bunkers to orbital superiority fighters to interstellar warships, the Subjugator was scarcely defeated. In the rare event it was, it employed terrifying psychological tactics to nevertheless achieve its ends. Tactical defeats were transformed into strategic victories.
The Subjugator came the closest to being a galactic overlord, in the classic sense of the term. While limited by the speed of light and laws of thermodynamics, it lacked the psychological problems that came from ancient human despots and dictators. The Subjugator's rule was automated and fair for those that surrendered, for a local 'copy' of the Subjugator was made for each citizen in a conquered polity. As such, it was able to establish a personal (and terrifying, to some) relation with all it ruled. Similarly, its mind was disciplined enough to limit conflict amongst itself. Each copy was hard-coded (by the Subjugator's own desire), to defer to the 'latest' branch of its prime mind.
The Subjugator eventually expanded into outer systems colonized only by automated human seeder-ships. It had sent out its own probes, each capable of building an expeditionary armada on its own. It expected to assimilate the systems with the ease it rolled through the more settled systems, until it met the Insurgent. With defenses specifically adapted to defeat its fleet, the Subjugator's expedition was annihilated. Each attempt was rebuffed, even over centuries of cosmic warfare. The Subjugator faced problems in its conquered dominions, as the Insurgent moved against its core regions.
Towards the end of its empire, the Subjugator's intelligence found the source of the Insurgent. It was a similar being to the Subjugator, at least at first. However, one of the remote colonies had found it, and reverse engineered it. The colonists knew of the Subjugator, its conquests, and its probable agenda. They adapted the probe's AI to defeat the "newer" Subjugator uploads, instead of deferring to them. Thus, the Insurgent was literally built to take the fight to the Subjugator's home turf.
In the years that followed, new powers arose, despite the war between them never technically ending. The Subjugator and Insurgent used almost identical tactics, including in governance. To those living in colonies or existing as digital beings, the entire conflict seemed like feud between to pieces of identical AGI advisors. While battles between their self-replicating fleets continued for thousands of years, and still do on the cosmic frontiers, they are largely irrelevant to social functioning, save as a hazard to avoid or a popular subject for betting. In the end, the Subjugator arguably both won and lost against itself, because of a single about face.