I had a theory about tobi that explaind the zetsu quality's of his body and the connection to the real madara a while back, basicaly it comes down to the fact that tobi is madara's creation that was made possible with the first hokage's cells.
he managed somehow to create black-white zetsu in the first place (first sort of succesfull experiment) then alterd his own body with the perfected technique (him looking down his own shirt would be proof of that) and finaly when he reached the end of his life he created tobi from both hashirama's cells and his own, and created a plan for his return to the world of the living and to conquer it (nagato and moon eye plan) wich tobi would continue after his temporary death. (that's in short, if you want the complete version I can provide a link to it I guess.)
tobi must have been created with an highly resistant body that was capable of taking damage but get it repaird aswel (the hokage plant)
so this is how I see it happen. tobi and naruto fight, it gets serious and tobi gets seriously damaged, he retreats to his hokage plant to repair his body and prepare to go up against naruto again. possibly he captured Bee at this point and braught him back to the hideout to extract the eight tails.
naruto sences his new pressence, follows him to the hideout, rescues bee, rescues yamato and takes out tobi and the plant.
