The End of Naruto #2
Here's my order of events for the final arc of Naruto.
1) Naruto will rematch with Nagato, in this fight we will see Naruto vs the man who possesses all the powers of the Six Paths of Pain, boosted by an ability to regenerate. Nagato will therefore be stronger than in their previous confrontation. This fight will allow Naruto to fully develop the skills of using the Kyuubi's chakra cloak. Needless to say, Naruto will win.
2) Sasuke will rematch with Itachi, in this fight we will Sasuke fighting an Itachi at full power, with no risk of blindess, no illness, boosted by an ability to regenerate. Itachi will therefore be stronger, and will not be holding back as he is controlled by Kabuto. This fight will show off the abilities of Sasuke's EMS, the secrets of which will be revealed by the end of the fight. Needless to say, Sasuke will win.
3) At some later point - not neccessarily straight away afterwards - Naruto and Sasuke will have a showdown. It'll be an awesome fight but at the end of the day they'll be equal, Rasengan to Chidori, Yin to Yang, light to dark, blow for blow Naruto and Sasuke will share mutual annihlation if their fight is allowed to reach its conclusion (as predicted by Naruto). But it won't, Tobi will appear when they are both weakened enough, he'll extract the Kyuubi from Naruto and the EMS from Sasuke leaving them both on deaths door. Tobi will then revive the Juubi and use the sealing technique to become its host, but get owned by Kabuto at the convenient but necceassary moment of vulnerability in the process. Tobi dies and Kabuto reveals his true motives at last, desiring to use the Juubi to accomplish his goal - whatever that might be.
4) The loss of his EMS will have 'opened Sasuke's eyes' so to speak, having being stripped of his sight and most of his power he'll realise the futility of his ambitions of revenge and hatred, he'll turn good again. Yay. Together he and Naruto, both ridiculously weak, will somehow manage to overcome an incredibly overpowered Kabuto - because they're the main characters. This will only be possible because that's the whole idea of Naruto, that through determination you can beat even the highest odds. For example Rock Lee who possesses only Taijutsu can still almost defeat the jinchuuriki Gaara in Part 1. So too at the end of the series can Naruto and Sasuke, without their respective unfair advantages over others (the Kyuubi and Sharingan namely), defeat the main bad guy. They'll both retain the abilities they earned through hard work, Naruto will be at the level he was when fighting Pain (minus Kyuubi) because he'll still have sage mode, and Sasuke will still be at the level he was when fighting Itachi (minus Sharingan and the Cursed Mark) because he still has all the speed and stuff developed over the timeskip. Rasenshuriken and Kirin will be their most powerful moves.
5) They'll both survive, there will be no more tailed beasts, no more curse of hatred between the descendants of the Sage. All the problems between villages will be resolved, Jiraiya's dream of people truly understanding one another will be achieved, peace will ensue. Naruto will be elected leader of the unified Shinobi world, and Sasuke won't be bothered like the Uchiha ancestor or Madara were, because he's freed from their hatred. The end pairing will be Naruto with Hinata (who he'll love despite her shyness) and Sasuke with Sakura (who she'll love despite his blindness), because they both need to have families for it to be a happy ending, and if Naruto ends up with Sakura then Sasuke's ending isn't happy, and neither is Hinata's.
The only thing I can't guess at are the parts played by 'Itachi's gift' or 'Naruto's secret jutsu'. I imagine Kabuto's sixth coffin - whoever the hell it is - will be used for Tobi's destruction, and Kabuto's 'that jutsu' will be relevant to his true motives. Feel free to comment and tell me what you think.