One of the most critical things for all SHs to keep in mind is a sense of consistency within their own plots, and with their own NPCs.
While it may sound funny to apply to a fantasy or sci-fi setting, it's important to maintain a sense of realism with the elements you control. What that means is that your NPCs are treated like three-dimensional, real people. They have wants, needs, fears, etc. They have pasts, and lives, often beyond what the players get to see.
Keep those lives in mind when you narrate the actions of your NPCs. Your villains should have a reason for doing what they do. They may also have had to work a little to set up the scenario you introduce the players to, and that prep matters when determining what the villain is capable of, and what impact the players can have on those plans.
Essentially, don't think about the NPCs in your session, think about them outside the session, to make sure there's a logical path from where they were and who they were to where and what they are when the PCs meet them.
Understand, you don't need to write a full biography, just have a quick synopsis in mind for things like motive and rationale to complete the character, and avoid making two-dimensional cardboard cut-outs that only exist for the players to chop down, or rescue.
In some cases, you don't even need to have prepared the full backstory, just be prepared to think of the details when they become relevant. For instance, if the PCs try to reason with the bad guy, rather than attack him, you should be prepared for how she will react. If they decide to not only rescue the wounded soldier, but get to know him and try to help him recover from his experiences, you should be prepared for that. Every NPC has the potential for becoming a lasting facet of the IC world, and for that reason, you should be prepared to predict how they'll behave, even in situations you haven't yet prepared for.
The same goes for your plot elements. If there's a fire in a warehouse, you should know how it started. If a plague reaches the city's water supply, you should know how it can be cured or treated, and how it will spread (touch, fluids, through the air, etc). Treat all the elements you introduce to the world, and to the PCs, like realistic things, even in cases where they might not have a real-world equivalent.
Anything you haven't directly planned for can often be realistically determined by following a logical path from what you already know. A poorly-payed mercenary might choose to run after seeing one of his colleagues cut down quickly by a talented PC's blade, rather than stay and fight a losing battle. By contrast, a freedom fighter might fly into a rage and attack the same PC, even if it seems like a lost cause. Fire magic in a dry, wooden structure might have unintentional consequences, as would ice magic underwater.
In short: be ready to provide realistic reactions of your NPCs and the surroundings to whatever choices the players may make; even the ones you can't predict.
Doing so will satisfy all Three Fs at once: fairness, in that your villains will have to follow the same rules when setting up their dastardly plans against the PCs; freedom, in that it allows the players to make any choice and have the IC world react appropriately; and fun, because a realistic world gives players a sense of understanding and expectation for what can happen based on the choices they make.
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