Here is what I think...
Madara and Tobi (Izuna) had a plan from the very get go. Izuna gave his eyes up so Madara can get stronger. Izuna ending up dying later and Madara realized he needed to become stronger. He figured, if he could get the dna of the first hokage, the he could awaken the rinnegan since the sage of the six paths is the ancestor of uchiha and senju.
Madara and the first hokage fought and Madara somehow retrieved some dna from the First Hokage and awakened his rinnegan. Somehow Madara dies, but before he does, he resurects his brother using the rinnegans resurrection technique. Now his brother takes Madaras eyes and puts them into nagato since he is a bloodline of Uzumaki meaning he can use the rinnegans power.
Tobi from here goes and kills all the Uchihas with Itachi except for Sasuke. He did this to get the Sharingan Eyes to make him and his brother even stronger, he just had to revive his brother.
Nagato was just a tool to eventually resurrect Madara himself after they captured all the 9 tailed beast When Madara was resurrected, he talked of how Nagato must of grown and then later was shocked that he was resurrected by the Impure world technique and not Nagatos technique.
The brothers plan was to seal the 10 tailed beast into Madara and make him even more powerful, so they would surely be the strongest. Since the plan was messed up by Nagato dying, Tobi decided to take the Rinnegan and WAS going to make Sasuke a tool by giving him the Rinnegan.
Plans were messed up here yet again when Kabuto resurrected Madara in front of Tobi's eyes. He couldn't wait to give the Rinnegan to Sasuke anymore so he took them himself so that he may resurrect Madara after he gets the 8 and 9 tails before Kabuto can wipe Madaras mind and make him his puppet.
Now that Kabuto has resurrected him, Madara believes Kabuto is on his side, but as Kabuto states, the fake Madara (Tobi) will not got with the plan. I believe when Tobi finds out Madara has been resurrected, he might try to use the rinnegans power to revive Madara fully instead of being a zombie.
My head is spinning its so confusing!!
