Berries, and the story introducing its own concepts

I have wondered about the experience when an author said/wrote that the story (or a character) took over and began introducing its own concepts.

Perhaps I've had that experience during the times when following-the-logic introduces something I had not actually conceived of before that moment. For example, where did the concept come from that Mrs. WhosyWhatsit needs to trust Alexa before telling her why she knows about the mystery man? It had just barely occurred to me that Mrs. WhosyWhatsit even knew about the mystery man.

The challenge, of course, is IF Mrs. WhosyWhatsit must trust Alexa, then WHY is that the case, and what is the whole backstory for this situation? Figuring this out often involves me pacing from the kitchen through the dining room into the living room, back and forth. While working on this particular instance, I found munching blackberries to produce more ideas than munching on blueberries. A noticeable drop in creativity happened when I switched to blueberries (go figure).

Berries, however, did not solve the dilemma. I had to resort to Curio (a nice mind-mapping program for Macs). It works well for putting concepts in little colored boxes and moving them around till they make sense.

Later, while cooking dinner, the final piece of this side-story fell into place. It even allows me an opportunity to tie into the planned third story in this triptych!