Even with all these branching options, all chapters must have a single starting point. If you have multiple alternate storylines that exist over the course of several chapters, you need to use FLAGS to resume the correct story line at the beginning of each chapter.
Here are two example chapters which deal with storylines.
These flags are exactly what we have been talking about above - things that set what choice a player may have made in an important decision. These last across chapters and can be referenced between them, but we canNOT end in the middle of a branch.