Maybe the samurai armour is not what it seems. It's actually a disguise for an ancient and powerful demon. Naruto, thinking he's getting an advantage, unknowingly unleashes the demon. Now he has to team up with his enemies to reseal the demon while still wearing the armour that's now part of the demon.
One idea could be Naruto discovers an ancient samurai armour in a hidden cave. The armour has special powers that enhance his ninjutsu. As he puts it on, he feels a connection to the samurai of old and starts to incorporate their fighting styles into his own. He might use the armour to face a new and powerful enemy that is immune to regular ninja attacks.
Perhaps the plot could start with Naruto finding an old, tattered scroll that shows the adventures of Samurai Jack. Naruto becomes obsessed with Jack's story and starts to train in a way that combines his ninja training with what he thinks Samurai Jack would do. As he progresses, he starts to have visions of Jack's world. Eventually, he finds a way to cross over. In Jack's world, Naruto uses his ninjutsu in creative ways to help Jack in his fight against Aku. In return, Jack teaches Naruto the art of the samurai, and Naruto brings these new skills back to his own world to face his enemies in a different way.
One idea could be a story where Naruto discovers a hidden samurai clan and has to learn their ways to defeat a new powerful enemy. Maybe he has to master their unique sword techniques.
There could be a plot where the ninjas in the Naruto world are being influenced by Aku's dark magic. Samurai Jack, with his unwavering sense of justice, teams up with Naruto and his friends to break the spell. They then travel to Aku's lair to take on Aku directly. Another interesting idea is a world where the Naruto characters are re - imagined as samurai, and Jack has to train them in the ways of the samurai to face a new threat that combines the worst of both their worlds.
One idea could be that the Samurai Girl is on a mission in the Ninja world and crosses paths with Naruto. They initially have misunderstandings due to their different cultures but gradually learn to work together. For example, she might be tasked with retrieving a stolen samurai artifact that has ended up in the hands of a rogue ninja. Naruto, being the helpful and curious person he is, decides to join her in the quest.
A plot twist could be that fem Tsukune is actually a long - lost relative of a powerful Naruto character. Maybe she has some special bloodline that links her to someone in the Naruto universe, and this discovery changes the whole dynamic of the story.
Perhaps Naruto discovers that Sheele was sent to his world by an enemy as a spy, but she has actually fallen in love with the place and the people, especially Naruto, and she has to prove her loyalty. This would create a lot of drama and tension in the story.
A possible plot twist could be that Tsuyu is secretly related to one of Naruto's enemies. Maybe she discovers this during the course of a mission and has to decide whether to side with her newfound family or continue to be Naruto's ally.
A possible plot twist could be that Naruto's blindness was actually caused by an enemy's secret jutsu that was meant to be permanent, but it turns out that Naruto's Uzumaki bloodline has a hidden ability that can reverse the blindness under certain conditions. This would add an element of mystery and hope to the story.
One possible plot twist could be that Naruto was cloned by an enemy to infiltrate the Leaf Village. But as he grows up, he starts to develop his own sense of self and loyalty to the village, causing a conflict within him. Another could be that the real Naruto is actually alive somewhere else, and the clone Naruto has to find and reunite with his original self.