It's Sasuke's & Itachi's mom. Calling it. It would explain why Itachi is taking care of a baby in the night.
Listening to Jiraiya earlier on, you get the clear impression that most people think the 9-tails JUST got loose for no real reason. Either that, or they might have known pregnancy weakened the seal. In either case, it would explain the cold or outright aggressive behavior towards Naruto even for people who know he was the 4th's son; Kushina was the host, so in the minds of people outside of the loop, the 9-tails was loose either because she was too weak or she let it escape of her own free will. Meaning her son, also a host, would be just as weak or uncaring about the village's safety.
Anyway, since no one realized it was actually a 3rd party that brought this about, the person could slip back into society if things didn't go to plan.
Now Madara is in a man's body now. You might be wondering how he could be both Sasuke & Itachi's mom and another Uchiha (probably Tobi). Well, how did he get into his current body? I believe he has a mind link to every Uchiha, allowing him to see through their eyes and sometimes take over their body.
This theory hits a brick wall if their mom wasn't a blood Uchiha, but I'm really expecting a reveal by the end of this story.