Fridge Horror: All those zeds you decapitated? When the mask gets returned, we can assume that they become regular dead innocent folk.Nice one, John.
Worse, we never see Uncle comeback, implying that the poor guy stays dead.
Combined with Offscreen Inertia: after John becomes a zombie, we're given a brief statement that we need to help set his soul to rest. Because this is a sandbox game, you can never "end" it. Unless something happens after we achieve 100% Completion and stop playing the game, John's soul will never be set to rest, and he'll be doomed to spend the rest of his existence as a zombie.
Yet another Fridge Horror: Complet all the Missing Persons activities before completing the story.Once the apocalypse ends, they presumably return home to their (remaining) families. Once the apocalypse starts again, how do we know they weren't eaten by zombies, rendering Marston's helping of them in vain?
How about the rescue missions? After John is turned zombie, how do you think those he rescues see him? Here comes a zombie, riding a (possibly) flaming or skeletal horse, shoots other zombies, and then proceeds to offer them a ride. It's surprising any of these people decide to get on the horse. Especially as Zom-John can't really talk.