How to introduce a previously hidden faction without creating plot holes?

Question

I've been planing out a sequel series to my trilogy, which has a secret society called Nukui-Paub spearheaded by the sequel trilogy's primary antagonist Ma'dtuth, who draws inspiration from Vandal Savage, Apocalypse, and Dragon Ball GT's Baby. Ma'dtuth is the former ruler of an offshoot of humanity called the Bassirid (which he aims to resurrect via time travel shenanigans) as they once ruled the hyper-advanced nation of Dosham (what we now call Atlantis) with descendants that influenced the development of all Indo-European and Afro-Asiatic cultures. It's suggested that Ma'dtuth used Nukui-Paub as a means to shape the history of various ancient Near Eastern civilisations in the name of building a utopia embodying his Darwinian principles.

But, the problem is neither Ma'dtuth nor Nukui-Paub even get a passing allusion or mention in my original series. I fear that potential readers (if I'm lucky to have any) will find the idea of both entities spending God knows how long lurking in the shadows rather than playing a significant role in the last trilogy hard to swallow. Or worse, think that I pulled both ideas out of the deepest reaches of my colon.

The worst example I can think of is Halo's Forerunner Saga novels (a prequel series set millennia before the events of the games) reveals that millions of years ago, that humans once ruled a galaxy-spanning empire that rivalled the Forerunners in power… and nor do 343 Guilty Spark, Cortana or any Bungie-era background materials mention this at any point (considering the previous two's vast knowledge on everything Forerunner-related). Even worse is that after the Forerunners devolved mankind back into the Stone Age, they could create vehicles such as airships and steam-powered ships, which would have been beyond impossible for Pleistocene humans to develop. And pre-343 media never even depicts prehistoric humans as having the capacity to create such things.

So, when all is said and done, how could I avoid making such a revelation come off as half-baked?

Answer 1

First, can you even believe why these two particularly powerful characters would remain hidden? If if you can't convince yourself, you won't convince a reader.

Second, does it have to be in the same setting? Your antagonists clearly do not. How about your protagonist and support characters? Can you separate them from your world and plop them down in a different story. You may need a new stand alone novel or trilogy to contain this story.

Answer 2

First, you need a reason why they did not show up in the first trilogy: was it set on a different continent, where the Nukui-Paub were not operating? (Have they decided to expand, or has your protagonist moved?) Were they working against the antagonist of the first trilogy? (This may let you "redeem" a popular villain from the earlier books, giving them a sympathetic reason for their actions) There is a reason why lots of books or TV shows expand geography as they go: it's the principle of "Big Fish, Small Pond" at play, and moving the protagonist to a bigger pond from one which the bigger fish overlooked or ignored.

Next, pick out all of the unsolved mysteries, unanswered questions, and moments of "fridge-logic" (e.g. ""but why did that character happen to turn up at just the right time to save our heroes?") in your old trilogy. Then examine each one very carefully, and see if there are a small number which could reasonably be explained as related to your new villains, without causing more plot holes.

If you do this right, you may be able to convince the reader that they can see the shadow of the Nukui-Paub slithering around in the original trilogy as a hidden faction.