-( Story related, cannot be missed )-
Much like Dorothy, you are given the ability to spare, embrace, or charm Sean. Embracing will nullify the following trophy, if you are trying for it this run:
The Hidden Trophy trophy in Vampyr worth 253 pointsContinue playing to unlock this hidden trophy
If you wish to have as little threat to your ability to level, simply spare him and you shall be able to carry on by leaving the Night Shelter. This will shift you directly into the final act of Chapter III, where you discover a corpse with the Paxton sisters and Ichabod.