One of the oldest tricks in the book to flesh out a game is to take the players own paranoid fears about NPCS and the setting and making it 'real'. I've spent hours just letting players speculate on the state of a game and took notes giving me ideas on how the badguys will act (or how the players expect them to act) down the line. I call it Paranoia Kabuki Theater?
I learned later in my GMing career that if the NPCs start doing seemingly random things the players will try, desperately to find a overall theme to WHY they are doing what they are doing. And a quiet GM during player chat can get loads of ideas if you make little changes to your plot. Part of his discover was just how disappointed player will get if their theories are always wrong. I use to dream up my badguy plans in my head and then give what I thought were useful clues to the players. Often it wasn't enough and they got completely different ideas about what was going on. It was only later I figured out how to give players enough information to lead them towards my concept of the plot.
But to prevent total player disconnect to the ongoing story I started making their theories correct. And HO-BOY was that fun. Assassins being hired to stop them from saving the Presidents Daughter? More likely than you think! He's steeling the Overthruster to build a spaceship that can enter the 8th dimension? Why not? And the players pat themselves on the back because they were right, and I didn't have to come up with the plot twist for the night.
Now...that's old hat. So why do I call it Paranoia Kabuiki Theater? For 2 reasons: The first is the pacing of traditional Kabuki, called Jo-ha-kyū, it represents slow, break, rapid. Such as slow hints early in the game, a masive break or ah-ha moment by the players when they 'figure' it out. And the rapid deployment by the GM of their theory by the NPCs allowing the players to act on their information fast enough to be useful.
What I'm getting at is that you need to take your time building up with the players. Give them small subtle hints, and give them plenty of down time between clues (events, even if random) to build their opinions about the game. Usually give them 'planning sessions' where the PCs can talk to each other. This is important. The next part is the "break" or breakthrough when the PCs declare a theory. This needs to be handled fast, give them another clue to confirm the theory you like and give them a motivation to put this informatin into their own plan of action. Finally make sure the PC's get quick resolution of their theory before they have time to rethink it. Otherwise, the disappointment sets in that they might not be right and or they start looking for more shadowy alternatives.
The end result will be a very play like nightly session with a good climatic resolution. This is great for investigation games with an episodic feel. Like Monster Hunting, WoD faction fights, Exalted politics, etc. Longer term dungeon crawls and exploration doesn't benefit from this.
The second reason why I call it Kabuki Theater is the over expressiveness you need to use with the NPCs. This comes from describing them, showing off specific colors and actions to play up their behavior, and finally very specific if stereotypical methods of behaving. The end goal is your NPCs should signal the players their intentions. Someone who is supernatural should have a green cast, strange reactions to the world, etc. Primal marks and masks. A fierce general should have the bearing of a Lion, wild hair, dark piercing lines. Etc. It's all makeup, but damn if it doesn't help. This is key if you want to guide the players theories in something of a right direction. I've learned that playing up 1 or 2 aspects of an NPC help me give them a clear indication of friend vs foe.
Yes, it's a good thing to sometimes play against stereotypes, but that's more advanced techniques. They need to be used sparingly actually. Too complex games can sometimes hurt the overall fun of the session. And it causes a strong sense of mistrust and player anxiety, IMO.
But, then again I just want to dress up in costumes with wild make up. Dunno. Either way, use the players paranoia and make those NPCs over the top. It helps.