ive just completed the game and enjoyed it up to destroying the military base. the storyline made perfect sense by reading the info from the the glow which mentioned that the experiemnts with FEV are taking place in a milatary base north which the brotherhood wanted me to check out anyway, so i blew it up thus ending the source of the mutants. all this makes sense. however afterwards nothing actually led me to the cathedral, i knew where it was so i went there and ended up killing the master and finishing the game. how exactly are you meant to know the master is at the cathedral and who exactly is he and what was his connection to the children? non of these were answered and im guessing i must have missed something.