From what I can see this story is a lot about reincarnations and spirits. Now I understand why the story shifted to the past, although in my personal opinion I would have preferred that these last two episodes had been the start of the anime and not part of the episodes near the end.
That way everything would have made a lot more sense and the viewer’s emotional connection to the characters wouldn’t have been lost, at least not necessarily.
It’s a really good story that’s finally starting to tie up some loose ends. I’d even say there are subplots here that could have their own separate anime.