Each Chapter is better then the last.
I think it would be interesting that after besieged to have a few different story arcs, such as Ungimp Tim, Adventures in Promies, Escape from Dynamis, The Search for the Avatars, but to have an underlining enemy through each story that you slowly learn more and more about.
What I have in my mind is an enemy that isn’t represented in the game so it gives you more freedom about how you want to put them together.
I imagine it being something like a mime, not the French kind, but the type in other FF games. Where you could have like 1 or 2 members run into them here and there and each time they fight one of the mimes it learns all or some of that person’s abilities, to were they become stronger each time they meet leading up to one hell of an epic battle in the end

. (I guess that is kind of like the Arch Angel battle)
Also could have someone be replaced by a mime and they could have their own little side adventure trying to get back to the group. Or have a discovery that the three Nations have hidden/classified the information about the group of mimes (that’s why no one has seen or heard of them).