Writing and the X Files...

In the last few weeks I have done some major plot revision on book #2. I was hoping to explain the process and in pondering how to put it into words I thought of my favorite old TV show, X Files. Especially since I have heard there is a new movie coming out.
As for the TV series, there were two types of episodes in X Files.
The “regular” episodes and then the “Conspiracy” episodes.
They showed interchangeably sometimes you’d get three weeks of one type and then two of the other but rest assured the conspiracy ones were always interspersed throughout the season. Sometimes I wish I could get the box sets of all nine (I think) seasons and just watch the conspiracy episodes from beginning to end to see if I could figure out what really went on.
So now to the gist of the post.
When I wrote the second book of Dominion Day, the book covered a number of years, ten I think. And I had regular scenes as well as scenes with the main antagonist and his buddies. There was also the story of a minor char intermingled in these scenes. It was a good story, however after the first Storymakers conference, my best friend suggested that the second book encompass just one of the main characters short experience, and leave the rest of the story to the fourth book. I totally agreed and went home. Pulled the book apart chapter by chapter laid them on my gigantic dining room table and separated them like she had suggested. I also altered the first book to end in a different but much better spot.
So as I have sat and stared at the plotlines of book #2, I began to realize that it wasn’t a solid plot; too many holes, too many inconsistencies.
(BTW, Book # 3 is a different character and story line, I never had problems with that book. )
A couple of days ago I realized what was wrong, I had the bad guy in both stories spaced over 16 years. There’s no way Noble would let this guy live for that long, I realized, and it made my story weak. So like I have desired from X Files for so many years, I separated the bad guy scenes from the regular scenes and I condensed the bad guy in the story into one book completely removing him from book #4. With that change it allowed me to create a solid story arc, with a beginning middle and end. I also began to think about my bad guy; who is he, why is he bad, what does he want to accomplish, how will he accomplish said goals? And suddenly it clicked, the bad guy became more of a real character to me and the reasons and other things began to appear. So now with the second book plot firmly in place I am ready to begin the rewrite.
Oh and book #4 you ask… I have ideas already, and plenty of scenes, and this time the antagonist is already firm.