Other than characters, the most important aspects of any successful book are the plot and story. First, let's talk about the difference between those two words. If you look them up in the dictionary, you'll come away thinking they are synonymous in the world of literature. They're not.
PLOT: Simply defined for our purposes as The Plan that drives everything in your book.
STORY: This is the narrative of how the characters behave and the events they live through (or don't live through) in your book.
Let me expand by using my V Plague series as an example. The PLOT of the series is that a powerful madman destroys the world with a bioweapon and turns millions of people into raging infected. The STORY of the series is the struggles of the characters to survive, seek revenge, etc. and what they go through in the process. This is where you will spend all your time, chronicling the characters' adventures and how they are changed by what they experience.
Without a strong PLOT, you'll struggle with the STORY. More importantly, without a strong STORY, the PLOT is meaningless. How many times have you read the synopsis of a book and the PLOT sounds fascinating, yet the result is boring? This is the result of weak story-telling and/or poorly developed characters. Plotting is easy. I can come up with new, exciting plots all day long without hardly trying. Turning them into a story, now that's the trick.
Okay, jackass, so tell us how to develop the story.
There are probably as many different ways to do that as there are stories out there. I know of authors who will spend weeks, even months, meticulously mapping out the entire storyline of a new book before they put a single word to paper. I know of some who draw inspiration from spitballing ideas. Which is the best way to do it? There is no answer to that question.
I have a completely unstructured, free-flowing process. Once I decide on the plot and the universe, I start thinking about who lives in this world. What are their goals and why? Who else is with them and are they a friend or enemy? Then, the engine that drives my writing... What can go wrong? How do I ramp up the pressure on my characters? From there, I'm off to the races, answering these questions as I write.
I, personally, do not have the patience to create a blueprint for where I want a book to go. If I ever tried to use that method, I have enough self-awareness to realize I'd be so stifled and constrained that I'd be unable to write.
But that's me and how my mind works. In no way does that mean it's right or better.
You have to find what works for you, and that will be your right way.