-Make Pain the final villain and end part 3 with Sasuke becoming the villain after fighting Naruto and gaining the EMS
-End part 2 with the death of Jiraiya, Naruto starting his Sennin Modo training and Sasuke joining Akatsuki after Itachis death
-Beginn part 3 with Naruto almost mastering Sennin Modo after 2 years, Sasuke killing 2 of the elders, abducting Killerbee and the Kage summit shortly after
-Sasuke fails to kill Danzo at the summit and Tobi declares war on the Gokage
-Sasuke recovers and fights Danzo as in the original
-Team 7 reunites, Naruto and Sasuke fight, Tobi arrives and retreates with Sasuke
-Kabuto approaches Pain and Tobi to increase their battle strenght with Edo Tensei with just the former Kages (excluding the Hokages), 7 swordsmen, Akatsuki members, Ginkaku & Kinkaku and a few Kekkai Genkai users
-Kisame is "defeated" by Killerbee and Ay and infiltrates the turtle island, but is killed by Guy
-The war extends over a week
-Sasuke deserts Akatsuki after learning about the true story of the shinobi world and then kills Kabuto
-Sasuke and Naruto fight side on side against the remaining Edo Tensei
-Guy and Kakashi fight Tobi and Guy uses the death gate to finish him off, but dies himself
-Nagato kills Kakashi and some other important characters, but is then killed by Naruto
-Everyone are exhausted and Sasuke turns against Naruto, they fight, but both survive, Sasuke loses his eyesight during the fight, but regains it after he awakens EMS
-Sasuke leaves while declaring that he will come back to start his revolution
Something like that...