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Another really useful tool here is foreshadowing and buildup. This is your first defense against the feeling of "awww, he just made that up": make it clear that the elements surprising the reader ...
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Source: https://writers.stackexchange.com/a/22226 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#3: Attribution notice added
Source: https://writers.stackexchange.com/a/22226 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
Another really useful tool here is **foreshadowing and buildup.** This is your first defense against the feeling of "awww, he just made that up": make it clear that the elements surprising the reader deep into the book, were present and significant right from the start. The reader only realizes that when he reaches the twists and surprises, but when he does, you want his reaction to be "Ohhhhh, _now_ it all makes sense!" rather then "Where the heck did that just come from?" If there are elements early on which we understand as not quite fitting, or there just being something _weird_ about them, these can click in to place later as the system is fully uncovered. That will make it feel much less as though you're "making it up as you go," and much more as though you're making exciting new discoveries and answering long-standing questions.