Probable bacterial infection. I suspect that the bacteria entered through the shell where you can the discoloration. I don't remember the story with this one, but reading about @chicken hawk 33
and his late term deaths made me think of it. Chicken Hawk 33, did you wash your hands with proper soap every time before you touched your eggs? Not sure if not washing hands could cause this or not, but I wash mine just in case.
Note: probably best not to use antibacterial soap because many of them have triclosan, which can be toxic to birds.
-Kathy
This is why I always wash my hands before handling eggs in the bator.