Well, in this kind of fanfic, usually there would be intense battles. Naruto is extremely powerful with his various jutsu like Rasengan. The Shinobi Alliance also has a lot of strong ninjas. Maybe the story would focus on Naruto having to face the combined forces of the alliance due to some misunderstanding. It could also explore Naruto's growth and how he tries to resolve the conflict without causing too much harm.
Sasuke is often a popular character in these fanfictions. He might play a role in helping Naruto against Madara or have his own motives during their battle. Kakashi can also be a prominent figure, perhaps using his Sharingan in a crucial moment to assist Naruto. Another popular character could be Hashirama, as his connection to Madara is a key part of the original story and can be further explored in fanfiction.
Another theme is redemption. Sometimes in these fanfics, Madara has a chance at redemption through his fight with Naruto. Naruto's belief in people's goodness can influence the outcome in such scenarios.
Naruto would probably win. He has an indomitable will and has always found ways to overcome powerful foes. His experience and the unique powers he might gain with the Rinnegan could give him an edge over Madara.
One interesting plotline could be Naruto discovers a new form that gives him an edge over Madara. For example, a form that allows him to nullify Madara's Sharingan abilities. Another could be Madara having a change of heart due to Naruto's unwavering belief in him. Maybe he starts to question his own motives for destruction.
In the 'ninja vs dragon novel', the outcome could be influenced by the plot. Maybe the ninja is on a quest to protect something that the dragon is threatening. If the story is about the underdog triumphing, the ninja might find a way to defeat the dragon through cunning and determination. They could set traps, use their knowledge of the terrain, or even form an alliance with other creatures to take on the dragon.
There would be a power shift. Since Madara was extremely powerful, Naruto - as - Madara would be an almost unstoppable force. Other villages would have to either ally with Konoha (which would be a difficult decision considering the situation) or try to find a way to counter this new threat. This could lead to a new arms race among the ninja villages.
If Naruto and Madara become friends, it could completely change the power balance. Their combined strength would be a deterrent to any potential invaders. On a more positive note, it could inspire a new generation of ninjas to look beyond past grudges. The younger ninjas would see that even the most bitter enemies can become friends. This could lead to a more unified ninja world where different clans and villages work together more closely. For example, the Uchiha clan might regain more trust within the Leaf village, and other villages might be more open to sharing resources and knowledge.
One possible plot twist could be that the real enemy is secretly manipulating the Shinobi Alliance to fight Naruto. So Naruto has to not only defend himself but also figure out who is behind it all. Another could be that Naruto discovers a hidden power within himself during the fight that changes the course of the battle.