Last night, I was writing a story and trying to figure out why a character would disband from a squadron of fellow warriors she liked. I skipped over it. I kept on until the character found herself trapped behind enemy lines with a comrade. My character let herself be captured by the enemy to make a diversion to allow the comrade to escape. So now I had to figure out why she would do that rather than just come up with a plan to escape with her comrade.
At this point, I realized that these two holes could be related. The squadron could have disbanded because the enemy killed one of the members with an incredible power, which ultimately broke the spirit and morale, causing the group to break up. My character could still want to fight against the enemy, but also want to gain that power she saw. So when she was behind enemy lines, she saw it is a perfect chance to save her comrade, as well as get close enough to try to acquire that power.
I really appreciate when stories are tightly woven. I don't mind them having big worlds or lots of characters, but I don't want the world so big that nothing is related. Characters need to recur (not all, but some). Story lines need to intertwine. If every time you try to answer a question, you make up an external source to solve it, you end up having a very jumbled storyline.
Try filling in the blanks later. If you get the stuff you know down, then look at everything you have, you may see patterns or connections you didn't notice before.