Is Richard Grey the Master? His audio log seems like it.
Most importantly, how come Ron Perlman said that the mutants went and razed Shady Sands? I thought I killed the source!
But MOST importantly: MY GUY SHOT THE OVERSEER! I was shocked! What the heck for? I know I had to leave, but I was going to do so peacefully. I liked that guy! WHYYYYY?!!! Why did I get what I assume is the bad ending? I did so much good! I was like, 'jesus of the wastes' or something!
EDIT: AAAAAAAAAAAHHHHH! I just read on the wiki that that ending happens with bloody mess! WHY DID I TAKE IT?! AHHHH! I wish I could pretend that didn't happen. I should have used the morph trait perk. DAMNIT!