Even though all the signs were flashing brightly that this was going to be the answer and I knew it was coming, I'm still disappointed by it. I guess easier answers to explain are well, easier to explain.
"Yeah, I found him buried alive, replaced most of his body with Shodai DNA/Zetsu stuff which made him look like an adult, brain washed him, taught him how to be boss, and when I died he inherited Akatsuki and my will to turn the world into a dream." -Madara