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.
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.
The plot should be engaging. It could add new twists to the Naruto vs Pain battle. Maybe introduce some new jutsus or strategies that make the fight even more exciting. Also, good fanfictions in this category usually have a good balance between action and the emotional aspects of the characters.
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 such a fanfiction, Naruto and Sasuke might win. They are both extremely powerful and their combined strength, like Naruto's Rasengan and Sasuke's Chidori, could overpower Madara.
You can try some popular fanfiction websites like FanFiction.net or Archive of Our Own. They usually have a large collection of Naruto fanfictions, including ones about Naruto vs Pain.
In this kind of fanfiction, Naruto being 'godlike' gives him a huge advantage. He might have powers far beyond his normal capabilities. So, Naruto would likely win. He could use his super - enhanced Sage Mode, or maybe some new jutsu that he has acquired in this 'godlike' state to overpower Madara.
In this fanfiction, 'godlike naruto' might have the power of absolute healing. No matter how severe the injury, he could heal instantly. He could also have the power to absorb and redirect any chakra - based attacks that Madara throws at him. This would make him almost invincible in the fight against Madara.