How do characters recover from stress/fatigue in story mode?
Recovering from Stress and Fatigue
At the end of an encounter or episode, or after a full nights rest you recover fatigue equal to toughness and stress equal to will power.
page 62 main rule book.
Plus don't forget the rally step you can do a Resistance or Discipline check to overcome some as well. Also while in story mode anytime you do roll the dice the universal boon/bane results still apply.