As James points out, plot and character are very closely linked. Plot is what your characters will do, so if you get to know your characters well enough, the plot will come naturally.
For me, this means the process of plotting a book is:
* Decide what kind of things I want to happen in it
* Come up with some characters that are likely to do that sort of thing
* See what happens
As an example, for my first novel I wanted to write about people who establish a colony on another world, outside of our solar system, and a war that starts there. So, I tell myself I need a main character who is likely to lead that kind of expedition. He's a military man, because in my world it is a military organisation that's most likely to be in charge of the expedition. Ambitious, because a lot of people would want this job and he has to get it first. I know I need internal conflict, so he has a fiancee who isn't quite as happy about leaving Earth as he is. That should help him have second thoughts.
And I need somebody to start the war. Obviously to do this, he needs to be in a position where he can attract supporters. A high ranking officer should be good enough; he can easily recruit from his subordinates. He needs a believable reason to start the war: altruism. He believes the universe will be a better place if he takes this colony and turns it into a strong military power, willing to settle disputes between other colonies that will follow it later. Why is this necessary? Earth won't do it -- some kind of tragic event in the past will make them think twice before they act.
Obviously my main character must oppose him. He doesn't like the idea of a military dictatorship. He believes strongly in democracy and individual freedom.
So, I have these two men, opposed to each other. The villain will have to act first -- what will he do?
And the story emerges from that question.