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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Alright I'm just gunna go ahead and say it. The Vex, or at least in one of the more popular theories of the Vex, because according to this theory: The entire universe, and everything that will and has ever existed that strings to our knowledge, is simulated and never actually did exist. The real universe is unknown to us, and a complete mystery. The only thing we can assume is that the Vex hold some kind of link to that real universe. So, the Vex, as being the race which created everything ever, seems pretty powerful. Halo's Flood? A Vex program. Alien's Aliens? Another Vex creation. Any evil race of any level of power? It was created by the Vex and exists only as a series of ones and zeroes. However, the creators of the Vex are technically the most powerful. But we don't know what they are, soooo.... [spoiler]and before any of you say "I rekt Atheon in 30 minetez u skrub th vex r wimpes", Atheon is [i]not[/i] the most powerful Vex mind there is. Not even close. Plus, Atheon doesn't even exist. [/spoiler]