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.
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.
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.
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.
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.
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.
The entire shinobi alliance might get involved in the rescue. They would pool their resources, such as intelligence gathering and combat skills. Kakashi, who has a history with both Obito and Naruto, could play a crucial role in devising a strategy to free Naruto. He knows Obito's fighting style and could use that knowledge to their advantage.
In fanfiction, Naruto and Obito could have a very complex relationship as brothers. Obito, with his troubled past, could be both a source of protection and a cause for worry for Naruto. Naruto's positive nature might initially be at odds with Obito's more jaded view, but over time, Naruto could help Obito see the good in the world again.