I spent a long time studying chemistry, and I'm always surprised at how something that seems so different from novel-writing turns out to be quite similar. To use an over-used metaphor, when characters have good chemistry, they behave a lot like chemical reactions.
In chemical reactions, there’s this concept of the energetic “state” of the process. You start with a couple of chemicals (reactants), and they have a particular energy determined by what they’re made out of. You bring them together in a test tube, and if they’re the right reactants in the perfect conditions, something drastic and irrevocable will happen, and they'll form something so unstable it can only exist for a few moments: the transition state. Then, instead of falling back to where they were before, the transition state becomes something new: the products. The energetic state of those products is usually lower than that of the reactants. That’s why chemical reactions happen. Energy flows downhill, but it has to go through hell first. This is how I think about stories.
When I’m starting a new story, the main character always comes to me in a “ground state.” I picture her in her element. It’s usually a single, mundane scene of her at work, on the bus or talking to a friend. Once I understand her in this commonplace way, I know what kind of people to put around her to get her out of her comfort zone. I know what will make her react. Only then can I get her into a high energy, unstable state where the story takes place.
This is where the exciting stuff happens. People fall in love and sacrifice and kill and betray. They form alliances they didn’t think possible and discover secrets about their lovers. When we get to the other side of the story, no one will be the same.
The key, I think, is that things aren't the same in a way that seems inevitable. The place where my protagonist ends up should be more “right” for her than the place where she started out, because that’s what happens when you create chemistry between characters. People get pushed out of their comfort zones, only to find out it’s what they needed all along to get where they belong. I don't think all stories work this way (nor should they), but mine do. What about yours?