In this kind of fanfiction, a possible plot development is that Naruto's body begins to reject the experiments, causing him great pain and internal conflict. His friends, like Sasuke, Sakura, and Kakashi, would have to find a way to reverse the effects. Meanwhile, Madara might be using Naruto as a pawn in a larger scheme against the other ninja villages. Naruto could also discover some hidden secrets about his own family or the origin of chakra during the experiments that would change the entire Naruto universe's understanding of things.
One possible plot development could be Naruto developing new and unexpected powers as a result of the experiments. For example, he might gain the ability to use some of Madara's unique jutsu in a different way. Another could be Naruto's friends trying to rescue him and in the process learning more about Madara's true motives and the nature of the experiments. Maybe Naruto also has to struggle with his own identity as he is changed by the experiments.
Well, a plot development might be that Naruto starts to have a connection with Madara on a deeper level due to the experiments. He could start to understand Madara's past and his reasons for doing what he did, which could lead to a moral dilemma for Naruto. Also, the Hidden Leaf Village might start to view Naruto differently because of the changes in him from the experiments. They could be afraid of him or see him as a potential threat, which would add a lot of drama to the story.
One possible plot development could be that after saving Naruto, Madara tries to mentor him. He sees Naruto's potential and wants to shape him into an even greater ninja, sharing his own knowledge and skills that have been honed over years.
Well, a plot could develop where Naruto is trained in secret by an old ally of Madara and Hashirama who knows about his heritage. This training could involve unlocking ancient jutsu that were lost over time. Also, his relationships with other characters like Sakura and Kakashi would change as they try to come to terms with his new - found family background. And there could be a conflict with the Akatsuki, who might see Naruto as an even greater threat or a valuable asset because of his relation to Madara and Hashirama.
Well, perhaps they travel back in time to the era when the ninja clans were first forming. Their fused presence could disrupt the power balance among the clans. The fused entity might try to introduce new ninja techniques or ways of thinking based on what Naruto and Madara know from their respective times. They could also encounter their own ancestors and have to deal with the moral dilemma of interfering with their family lines. Maybe they end up influencing the creation of certain ninja villages in ways that are different from the original history.
Madara could be experimenting on Naruto to understand the concept of the 'will of fire' that Naruto embodies. Madara has his own views on power and the ninja world, and Naruto's unwavering belief in the will of fire might be something he wants to dissect. He may think that by understanding what makes Naruto so strong in terms of his beliefs, he can either break that strength or use it to manipulate others. Also, Naruto is seen as a symbol of hope in the ninja world, and Madara might want to turn that symbol into something that represents his own ideals through these experiments.
One possible plot development could be that his friends, like Sakura and Sasuke, come to take care of him. Sakura uses her medical skills to try and bring down his fever. Another could be Naruto having fever-induced dreams about his past, like his lonely days as a child. Maybe he even hallucinates about his parents. It could also lead to a situation where the village is in danger, but Naruto is too sick to help at first, creating a sense of tension and urgency among the other characters.
One possible plot development could be Naruto finding strength within himself. He might start to question why his parents would do such a thing and through that self - reflection, he could begin to discover his own worth. Maybe he'll meet a mentor figure who helps him see that his parents' actions don't define him.
One possible plot development could be Naruto's struggle to break free from Orochimaru's control. He might have to face his inner demons and find new sources of power within himself. Another could be his friends trying to rescue him and having to fight against Orochimaru's minions. Maybe Naruto under Orochimaru's control is used to target the Hidden Leaf Village, creating a huge conflict.
One possible plot development could be Naruto's friends rallying around him. They might seek out medical help, like Sakura using her skills to stabilize him at first. Then, they could start planning revenge against Pain. Another could be Naruto having some sort of vision during his injury, perhaps about his parents or a new power he could unlock to defeat Pain in the future. And, his sensei, Kakashi, could take on a more protective role over him as he recovers.
One possible plot development could be Naruto facing internal struggles. He has always been Naruto Uzumaki, and now with Madara's DNA, he might question his identity. Another could be that the village starts to view him differently. Some might fear his newfound power, while others might see him as a potential threat. There could also be a plot where Naruto has to learn to control the new powers that come with Madara's DNA quickly, as an enemy emerges who can only be defeated with these new abilities.
One possible plot development could be that Naruto's new look causes confusion among his friends. They might start to question if he's still the same Naruto they know. Another is that enemies could be either more afraid or more eager to fight him, thinking he has some of Madara's power.