In such a fanfiction, the story could take a very dark turn. Naruto's ideals of friendship and peace might be severely tested. He could be forced to question his own beliefs as Obito and Madara have very different outlooks. Maybe Naruto would try to change their minds, but it would be extremely difficult as they are both very set in their ways of achieving a new world order through more extreme means.
A fanfiction story could start with Naruto being in a desperate situation where he feels that the normal path to peace is not working. So, he decides to team up with Obito and Madara. At first, they seem to be working towards a common goal. But then, Naruto realizes that their means are too extreme. For example, he discovers that the Infinite Tsukuyomi they plan would take away people's free will. He then has to find a way to stop them while still maintaining some sort of alliance. This could lead to a complex web of relationships and power struggles within the group.
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.
One common theme is power and ambition. Both Madara and Obito are characters with great power and strong ambitions in the Naruto series, and fanfics often explore how their relationship is influenced by these aspects.
The theme of redemption also appears. Given some of the actions of Obito and Madara in the Naruto series, fanfics sometimes explore if they can find redemption in their relationship with each other. They might try to make up for their past mistakes through their connection in the fanfic.
Well, one possible outcome could be that Naruto and Sasuke manage to defeat Madara through their combined strength and newfound powers. They might use their signature jutsus in a coordinated way that Madara can't counter.