How do you write a good twist?

Phil says:

I'm writing a sci-fi story as part of a game, and one thing I'm having trouble with is how to gracefully drop hints of an upcoming twist.

One character is set up so that everyone assumes he is a villain; the midpoint twist shows that he's actually just misunderstood and trying to survive; he actually has a lot in common with the player character.

I want to drop hints of this fact earlier on in the game. I think I can do this without it giving away the twist, but I'm worried that playe...