Check Everyone's Plans

Suppose you come up with this really cool character. He's got a great backstory, sweet costume, and amazing abilities. Now all you have to do is give this character something to do. Enter the villain.

You create the villain in response to the hero. The villain has some plan, usually complete with twists and turns. It's all well and good to move the story, but sometimes logic doesn't come along for the ride.

Suppose the villain leaves a cryptic note in the hero's room, which the hero has to decode and then follow the directions. When the hero follows through, he finds himself face-to-face with the villain, who gives a long, diabolical speech.

If the villain had access to the hero's room, why didn't he just skip all of that circuitous nonsense and just give his speech there?

When you have a bunch of characters in a story, each of them has their own motives and their own plans to achieve them. Check everyone's plans and make sure that they make sense.