1. The original history of shinobi is the truth.
A history where the Sage of Six Paths was a miraculous ophan born with the Rinnegan who mastered chakra, invented ninjutsu and taught it the world. Also known as the False Origin of Shinobi. There is no such thing as the Otsutsuki Clan, God Tree, Rabbit Goddess or Black and White Zetsu. Nor are there prophecies and transmigrants.
(read:
False Origin of Shinobi)
2. Tobi is Madara and Obito died years ago.
Madara was meant to die in the Valley of the End but was saved by a plant-like humanoid known as Tobi. It was one of the earliest experiments to reproduce the Wood Release and created a monstrosity that coudn't truly be called human anymore. As such, it hated Hashirama as much as Madara himself and saved his life for no other reason than that, wrapping its hollow body around the Uchiha to act as his lifesuit. To the wider world, Madara’s fate was an unsolved mystery lost to history.
Madara became a shadow of what he once was from his wounds but was able to live far beyond his natural lifespan with Tobi's aid. Together they learned of the history of the shinobi world through scattered tomes and tablets, including the Sage of Six Paths and the Ten Tails. They plotted against the hidden villages and would go on to join Akatsuki as its spymaster, believing that it would bring the vengeance that they sought.
And the Mangekyou Sharingan and the Eternal Mangekyou Sharingan have the
same jutsu for everyone who wields them without exception. Even weakened, Madara can use the power of his doujutsu and Tobi possessed a unique control over nature itself which made them a formidable team, even if they prefer to remain in the shadows.
3. Nagato is the final villain.
He was the first person to awaken the Rinnegan since the Sage of Six Paths himself. They awoke at the sight of his parents' death and its power tore out of the souls of their killers. But even as filled as anger and grief as he had been, Nagato feared this strange power so deeply that he unconsciously sealed it away until he could only touch upon a portion of its true strength. It wasn't until he lost his closest friend that Nagato could truly draw upon the Six Paths of the Rinnegan.
Nagato and Konan swore vengeance against Hanzo and chose to bring peace through force. At this time, Madara appeared before them and offered them aid and information. His knowledge enabled Nagato to summon the vessel of the Ten Tails, inspiring their plan to revive it as the ultimate weapon that would bring pain to the world.
Nagato mastered the Six Paths and created the Six Paths of Pain so that he could destroy his enemies without ever having to reveal himself (not because he was crippled). They chose to revive Akatsuki by gathering together the most powerful shinobi to capture the Tailed Beasts and recreate the Ten Tails. The plan to create an incredibly powerful weapons from the combined chakra of the beasts was true but the nature of that weapon was always meant to be Nagato as the Ten Tails' Jinchuuriki.
The Invasion of Pain destroyed the village but many of its people managed to evacuate beforehand or were protected by Tsunade (including Naruto and the toads) when the blow was struck. Naruto defeats the Six Paths of Pain but not Nagato himself who chose to retreat. They don't meet again until the climax of the war.
Orochimaru's dies for real, Kabuto joins Sasuke or dies too and Madara is the secondary villain, making Nagato the greatest threat in the series.
4. The Fourth Great Shinobi War is the Five Great Shinobi Nations against the rest of the world.
One of Akatsuki's long-term goals was to unite all of the minor hidden villages under one banner using their power, money and reputation. They incited the hatred towards the Five Great Shinobi Nations from the lives they’ve taken, the money they had stolen, the lands they had seized and all the countries they had destroyed in their wars. This Akatsuki Alliance represents all of the pain caused by shinobi and the fourth war is declared against the Great Five after the Kage Summit.
Nagato and Madara stole the research from Orochimaru's many hideouts to use the Impure World Reincarnation themselves, summoning all of the former Kages to serve as the most powerful individuals within the entire army.
5. Sasuke is female and Hinata is on Team 7.
Because, yes, I really do think Sasuke should have been a girl and I'd probably be rooting for Naruto the entire time.
Hinata's more suited than Sakura to be the heroine; her abilities make her significantly more useful from the beginning, her heritage makes her a better fit thematically, her character growth is similar but has greater meaning and she can easily fill the role of Tsunade's apprentice quite easily. But she would admire both Naruto and Sasuke, if for different reasons, and desire their acknowledgement without romantic feelings coming into play.
Hey, is there anyone who would have ended Part 1 with Naruto winning at the Valley of the End?
