This includes fantasy and sci-fi.
My choice is the Combine.
A multi-universal species from half-life so absolutely immense and powerful that they reverse-engineered earth's technology, upgraded far beyond human ability, brainwashed some humans and had them invade themselves. They did this and stomped all resistance within 7 hours. This was done by a backwater lesser combine city mind you.
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Forerunners, Precursors, Reapers, the Imperium of Man (wh40k). [spoiler]Reapers indoctrinate Imperium. Precursors use neural physics and stuff to assume control of Reapers. Forerunners support Precursors. Man gets tech fixed up and gain title of Reclaimers, Reapers invade the Warp and indoctrinate everything, resulting in a 'calming' phase (reverting to [Place name to do with souls?] ). Precursors leave galaxy and go to sleep in a holiday mini-galaxy. Forerunners build Halo Array (improved, designed with ability to focus on one species or type of, can be focused into a local area blast < galaxy for less genocide) then sit in Shield Worlds while Mankind is dealing with everything (see 'If the Emperor had text to speech...' for an idea).[/spoiler]