During the heat of battle, Obito suddenly kills sakura. Naruto states to Obito that he feels the same pain that he felt, and Naruto repeats those infamous words that Obito told Kakashi. During this Madara truly reveals the circumstances behind Rin's death and Obito betrays Madara aiding Naruto (maybe Sasuke) and the alliance in the defeat of Madara. During Obito's betrayal, Obito suffers severe damage to his body and Madara kills him, and Madara does some form of a 'super justu' that blows all of the alliance away and renders them useless. Then When all hope seems lost, Obito who was supposed to be dead does a jutsu on his dying breath that severly weakens Madara and Naruto finishes him off with his 'new jutsu'. Obito relays his trust onto Naruto and uses the remainder of his chakra to revive Sakura.
Naruto becomes hokage, but sets the tone for another arc and Orochimaru and Sasuke become the new main antagonists.
Scenario B: Pretty much the same as scenario A (except without Sakura dying) and Naruto hearing Obito's motives tries to bond with him and attempts to talk him out of it. Instead Obito simply laughs it off. After seeing this Kakashi decides that he has fallen too far into the darkness, and knowing he was the one partly responsible for the way Obito is now decides that he will put Obito out of his misery and Gai offers to help. The final battles are:
Kakashi and Gai vs Obito
Naruto and Bee vs Madara
Alliance vs Juubi
Gai seeing that Obito cannot be defeated easily opens the eighth gate. Kakashi attempts to use raikiri on Obito but Obito dodges it by warping into the dimension saying its useless. This actually turns out to be a diversion as Obito is shocked to find Gai waiting in the dimension and uses his finishing eighth gate maneuver to defeat Obito but does not kill him. Back in the real world Gai is dead, and Obito and Kakashi are on their last breath and Kakashi finally reveals to Obito why he killed Rin. On his dying breath Obito briefly realises that he was wrong, and states that he will be with Rin in the sky and dies. Kakashi dies from exhaustion.
In the Naruto and Bee vs Madara fight, the Hachibi is absorbed and Bee dies. Naruto seems like a complete goner until suddenly sasuke shows up. Naruto asking why he is here, sasuke states that the Man who knows everything changed Sasuke's mind and now he realises how much Itachi loved Konoha and how Madara is the root of all the Uchiha problems. The fight rolls on and Naruto and Sasuke using the similar team tactic they used in Academy finish off madara with an sharingan enhanced rasengan/rasen-shuriken sort of like this:
The Kages except Tsunade eventually show up and The alliance lose many of their comrades (choza, Shikaku, Inoichi, Neji, Gai, Kakashi, Tsunade) but eventually overcome the Juubi's godlike power with Naruto's help of course.
Sasuke returns to Konoha starts the New uchiha clan, and Naruto becomes the Hokage.
Scenario C:
The same as Scenario B except Naruto defeats Madara on his own, and Sasuke does not becomes the hokage. Sasuke attacks and kills Sakura
After he kills Sakura, Sasuke goes onto fight Kakashi. Sasuke ultimately kills kakashi but is wounded badly after the fight and encounters Naruto.
and sets the setting for Naruto vs Sasuke:
Which scenario would you prefer?