How to avoid plotholes when writing stories with dense mythologies?

Question

I've been brainstorming and working on worldbuilding, structure, characters and overall story development stuff for about 4 years now. Basically spending a lot of time brainstorming strong, well developed self contained ideas, only lightly juxtaposing ideas here and there.

Now, I've written my outline, my story involves stuff about a civilization in the sky and an a city below. There was a war that occurred involving the creation of a certain type of species as well as a time machine a scientist created (though at the time writing it, there was no real discernable reason why the time machine was created or what it would have been for... I was thinking or working that out later...)

Originally in the island below, there was also a civil conflict, which is part of the main premise of the story, though I never found reason for it to happen so it phased out, and I juxtaposed the war from the sky with the war below, merging them together.

So now, the war between those two species occurred in the island below, the island above would live the aftermath of it, as they inhabit the island afterwards...

Now in the stage of outlining, this created plotholes I'm trying to repair...

Is there any "order of operations" or objective rulesets I should take into account when worldbuilding to avoid plotholes or contrivances, and make sure when I write, I can make sure the plot retains a clean and organized structure?

I finished the first and second act in the outline, and found the third act won't have enough material and I need to add more ideas to the story (first and second half) to expand on the plot, is this bad, or will it still work?

The time machine is important to the plot, I'm just thinking about why it was originally created and what it could have been for.

Answer 1

I believe you answered your own question: Consider dumping artifacts onto both "continents" in earlier chapters from your time machine. Your third act can pull these artifacts together into some meaningful ... talisman. You will need a singular protagonist in this sort of complex world. There are numerous references on this site to the Hero's Journey to help define your hero (who will solve the clues, build the talisman, win the war ...). Use your protoganist's comrades to talk about "the way of things" to prevent long-winded info dumps (like this post).

Answer 2

Make the plot-holes problems your characters have to solve. The problems you are experiencing are problems with outlining. Once you start writing your story, using your outline for initial guidance, what your characters do and what happens in the story will fill in the gaps.

Later on as you progress with the writing you find you can abandon the outline and just find ways of combining the different plot elements into a richer and more developed story.

Always remember, you are a writer and you can always make something up. Go without fear. You're the one in charge of this world.

Answer 3

Some world-building authors base their story on real historical events; for example, A Song of Ice and Fire is basically mediaeval England. And if your storyline mirrors real events closely enough, that might prevent plot holes. For your purposes, the history of either evolution or technology could help.