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.
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.
In this kind of fanfiction, Naruto might first try to understand Obito's motives. He could see the pain and loneliness that drove Obito to his dark path. Maybe Naruto would try to convince Obito to give up his evil plans and return to the side of good. They could form an unlikely alliance against a common enemy, like Madara or Kaguya. Naruto's positive attitude and Obito's powerful abilities would make a very interesting combination.
The story could start with Naruto finding Obito in a desolate place. Naruto would be curious and approach him. Then, they would exchange words, and Naruto would offer his help to Obito. As they interact more, they might face some small - scale battles together against rogue ninjas or other threats. This would build trust between them.
Another way is through a prophecy. In the fanfiction, there could be a prophecy that only Naruto and female Madara together can save the shinobi world from a great disaster. At first, they don't believe it, but as the signs of the disaster start to appear, they are forced to work together. As they spend time together trying to prevent the disaster, they learn about each other's pasts, hopes, and dreams, which leads to a deep emotional connection.
In a 'naruto joins obito fanfic', it could start with Naruto being transported to a parallel dimension where Obito has already started his own ninja village. Naruto, seeing the potential in Obito's ideas but also the flaws, decides to join him. He helps Obito to correct his path. For example, Naruto could teach the ninjas in Obito's village about the importance of hope and not giving in to hatred. They could then work together to build a village that is a model for the rest of the ninja world, based on both Obito's and Naruto's ideals.
To develop Naruto in a crossover with Obito, you can put him in situations where he has to use his wits against Obito's Sharingan - related abilities. This would force him to become more strategic. Also, Naruto could learn about the Uchiha clan's history from Obito, which would expand his knowledge. As for Obito, Naruto's presence could make him confront the fact that his actions have consequences. He could start to see the value in the bonds that Naruto has with his friends and village, and this could lead to a change in his goals and values.
The main antagonist could be Madara. Even though Obito was once following Madara's plan, with Naruto joining Obito, Madara might see this as a threat to his grand scheme. He could try to manipulate events to drive a wedge between Naruto and Obito or directly attack them to stop their new alliance from achieving their goals.
In a fanfic where Naruto joins Madara, it could start with Madara convincing Naruto that his way of achieving peace is more efficient. Madara might show Naruto the dark underbelly of the ninja world that has been hidden from him. Naruto, being the naive but kind - hearted person he is, could be swayed into thinking that Madara's extreme methods are necessary for a long - lasting peace. But of course, this would lead to a lot of internal conflict within Naruto as he goes against his friends and the village he loves.
If Naruto merged with Madara, the story might take a turn towards exploring new forms of ninjutsu. They could start teaching the new generation their combined techniques, and the ninja world would see a new era of powerful shinobi. Also, their relationship could be a central theme, with Naruto constantly trying to keep Madara's darker side in check.
One way the story could develop is that Naruto would have an innate understanding of powerful Uchiha techniques. Since Madara was a master of the Sharingan and had many powerful jutsu. Naruto might be able to quickly master the Sharingan if he inherits it. For example, he could use it to enhance his combat abilities against stronger enemies. He could also have a different relationship with Sasuke. Maybe instead of being rivals, they could be more like cousins with a shared heritage to explore.