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.
Naruto could also use his chakra to resist. Since he has the Nine - Tails' chakra at his disposal, he might be able to disrupt the experiments. For example, he could flare up his chakra in a way that makes it difficult for Madara to continue with the procedures. Additionally, Naruto has learned various ninja techniques over the years, and he could potentially use them to counteract the effects of the experiments, like using shadow clones to create distractions or using rasengan - like attacks to break free from any devices used in the experiments.
One possible plotline could be Naruto discovers Madara's past in great detail and starts to admire his strength and the vision he once had for the ninja world. He might study Madara's fighting techniques and incorporate some of his strategies into his own combat style. For example, Naruto could be intrigued by Madara's use of the Sharingan and try to find ways to counter it more effectively based on understanding Madara's own approach.
One possible motive could be power. Danzo was always obsessed with having power in Konoha. By experimenting on Naruto, who is the Jinchuriki of the Nine - Tails, he might have hoped to harness the power of the Tailed Beast in some way. Maybe he thought he could create a super - soldier or gain some unique abilities from Naruto's connection to the Nine - Tails.
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.
He could combine the Rinnegan's ability to control gravity with his Rasengan, creating a super - powerful and hard - to - dodge attack.
In this 'madara kills naruto fanfiction', the scenario might be set up in a way that the world around them has changed. Maybe there are new rules in the ninja world that Madara has adapted to better than Naruto. He could be using the political or social situation to his advantage. Additionally, the writer may have given Madara a different motivation that makes him more ruthless and determined to kill Naruto, and through a series of carefully crafted events, he manages to achieve this goal.
One reason could be to weaken Naruto. In the ninja world, being a girl might come with certain social limitations that could hold Naruto back. Another reason could be for experimentation. Madara is always interested in power and knowledge. By turning Naruto into a girl, he might be testing out some new jutsu or power - related concept. It could also be a form of psychological warfare. Madara knows Naruto has strong relationships with his friends, and this change could disrupt those relationships and cause chaos within Naruto's circle.
Madara could also save Naruto by using his knowledge of the ninja world. Maybe he has some inside information about a plot against Naruto and he intervenes in time to stop it. He might have discovered a secret plan by an enemy group and takes action to keep Naruto out of harm's way. This could involve manipulating events behind the scenes or directly confronting the threat.
In this fanfiction, Naruto might join Madara because of some sort of time - travel or alternate reality situation. He could find himself in a world where Madara's actions seem more justifiable. Naruto, being Naruto, would still strive for peace. So he might try to guide Madara towards a more peaceful solution while being part of his group. This could create a really unique dynamic where Naruto is constantly trying to nudge Madara in the right direction while also dealing with the other members of the group who may not be as open to change.
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.