One unique plot twist could be that instead of Naruto being the one to finally defeat Madara, it's Sasuke who sacrifices himself to do it. This would completely change the dynamic between the two characters and the overall feel of the story.
Another plot twist could be that the Kyuubi, instead of helping Naruto, turns on him during the war due to some ancient curse or outside influence. This would put Naruto in a very difficult situation, having to fight against his own power source while also facing the other enemies in the war. It would also force his friends to choose between helping Naruto or stopping the rampaging Kyuubi.
In some fanfictions, a plot twist might be that the Allied Shinobi Forces are actually being manipulated by an unknown enemy within their ranks throughout the 4th Great Ninja War. This enemy could be using the chaos of the war to achieve a more sinister goal, like stealing all the tailed - beasts for themselves and using their power to rule the ninja world. It would add a whole new layer of mystery and betrayal to the story.
In a 'Naruto 5th Great Ninja War Fanfiction', the story could start with a strange phenomenon that begins to disrupt the chakra balance in the ninja world. This is a sign of the approaching war. As the war breaks out, the younger generation of ninjas, inspired by Naruto's heroics in the previous wars, step up to fight. They face off against a coalition of rogue ninjas who are being controlled by a shadowy figure with a vendetta against the established ninja order. Along the way, there are many battles, with each side using new and creative jutsus and strategies.
One interesting plot twist could be that some of the dead ninjas from previous wars come back not as enemies but as allies with a secret mission to end the cycle of hatred. They might have gained new powers or knowledge in the afterlife that can turn the tide of the Fourth Great Ninja War.
Well, one plot twist could be that a minor character turns out to be a powerful spy for the enemy. They've been hiding in plain sight all along, feeding information to the opposing side.
A really interesting plot twist could be that the cause of the Second Great Ninja War in the fanfiction is not what it seems in the original Naruto lore. Instead of territorial disputes or power struggles, it could be due to an ancient curse that has been awakened. This curse affects the minds of the ninja, making them more aggressive and starting the war. And only a few special characters might be able to figure out the real cause and try to stop it.
Often, fanfictions show Naruto growing even more in his understanding of the ninja world. He might realize that there are no easy answers to peace, and that sometimes sacrifices have to be made. For example, he could start to question his own ideology of always trying to save everyone.
One great plot twist could be that Itachi was actually working undercover all along to protect Naruto, not just for the sake of the village. In the original story, Itachi's actions were always a bit of a mystery. In the fanfiction, this could be revealed in a way that changes Naruto's perception of him completely.
One unique plot twist could be the Iron Dragon Slayer magic being a long - lost ninja art in the Naruto universe. For example, the main character discovers that an ancient clan had this power but it was sealed away for centuries. This would change the power dynamics in the Naruto world as it introduces a new type of combat ability that no one has seen before.
It could be a long - lost relative of Orochimaru. This person might have been secretly studying Orochimaru's forbidden jutsu and developed even more terrifying techniques. They could be seeking revenge on the ninja world for ostracizing Orochimaru.
Another plot could revolve around the relationships between different ninja villages during the war. For example, a secret alliance forms between two villages that were previously enemies, and they have to keep it a secret while fighting together against a common foe. This could add a lot of drama and intrigue as they try to balance their newfound cooperation with their long - held grudges.
A plot twist could be that Naruto is forced to be a ninja not in the normal sense, but in a virtual reality created by an enemy. In this virtual world, if he fails as a ninja, something bad will happen to his real - world friends. So he has to quickly learn the rules of this new 'ninja world' which is full of glitches and strange challenges. Also, he could be forced to be a ninja by a curse that was placed on him. This curse makes it so that if he doesn't complete certain ninja tasks, he'll slowly lose his chakra or even his life. It would be a race against time for Naruto to figure out how to break the curse while still fulfilling his forced ninja duties.