impossible mode:
Obito laments the loss of his last mangekyou sharingan to izanagi when sealing the juubi, then starts to experiment with his powers. He begins to boss around everyone, and regains the banana fan using a massive technique with all 5 elements to kill off all the fodder. The edo hokage, edo Madara, Naruto and Sasuke manage to survive with the respective jutsu and band together vs Obito. Obito makes 4 clones and has each use banshou tenin on the edo hokage and pull out their souls with human path. The original goes to edo Madara and uses rinne tensei, however he revives him in his old state as vengeance. Madara slowly dies without hashirama's chakra to support him. Then Obito kills off Sasuke last to torment Naruto, at which Naruto starts to break down.
Just as Obito is starting to perform infinite Tsukuyomi, Kakashi who's been regaining his stamina in kamui's pocket dimension teleports back. He takes off Obito's neck with Kamui, and while the juubi's chakra quickly repairs it, Obito who was already wounded loses control of the Juubi. Naruto regains his spirit as Kakashi reminds him of his words, enters sage mode and punches Obito's wounded face.
At this point, Naruto who has the tailed beasts' chakra and Obito who's juubi chakra spiralling out of control find themselves back in the dimension where Naruto met the bijuu. The Sage of Six Paths appears and recognises Obito and Naruto as the descendants of his older and younger sons. Again he chooses the younger son, Naruto, to carry on his will of achieving peace.
Obito and Naruto reappear. Obito is extracted, yet with his senju dna doesn't immediately die. Naruto finds himself possessing the juubi and also the rinnegan. He recalls all of the important moments of his life, and remembers that Jiraiya had entrusted the task of finding peace to him, Naruto realises what he must do. He finally reached a complete understanding as Nagato had wished, and realised that as Minato had told him, while there is the current system peace cannot be attained. In the end he decides that Sasuke's wishes to end the system are the way to go, so he seals himself and the juubi back into the moon, ending the lines of the senju and uchiha, but not before using rinne tensei to get back all of the other shinobi.
The 5 kage and reach the battlefield to find Kakashi holding Obito's body, who in his last moments regained peace as he realised Naruto's way and that he would be rejoining Rin. The 5 kage discuss on how to rebuild the world, as Orochimaru enters Obito's lair.
Now there are two alternate endings: either Orochimaru destroys Obito's sharingan store and gedo mazou inc yamato, Obito's body is cremated and his name is struck off Konoha's war memorial. Tsunade dies shortly after due to age related issues and Kakashi succeeds as Konoha's representative (the kage and shinobi system is no more).
or.
Orochimaru takes over Yamato due to the fact that his zetsu body allows the cooldown for his rebirth jutsu to dramatically decrease from 3 years to 1 day. He implants a sharingan pair in his eyes, and with the Kabuto chakra he took he enters dragon sage mode. Knowing that he know has the knowledge to awaken the rinnegan and summon the juubi again, he aims to spend the meantime rebuilding the sound village and continuing his neverending search for the truth, in preparation for his final assault on the shinobi system which brought so much pain and suffering.
edit: I know I'm vastly in excess of 20 pages, but a series like Naruto deserves a grand sendoff
