Advice from one writer to another: write whichever one u think u would enjoy most. Which one excites u more to think about and fills you head with ideas and scenes of what will happen in it? Pick whichever one does that I do like the sound of the second one because it is more unique. Making it free from the constraints of the story of the game will give you room to do whatever u want in the story to make it good, but it also means it will be a lot harder to write because u don’t have a backbone story to base the events and progress of your story off of Option one has been done many times (I myself am doing it, although I have written several stories not tied to the missions or story of the game) but is still great material for a story, so don’t go dismissing it just because it’s been done before; u can get great results from it if you’re creative enough to throw in some curves and real emotion and character building