Well, it could be for revenge. Madara has his grudges against the ninja world and Naruto is a symbol of hope in that world. By turning Naruto into a girl, he's trying to take away that symbol of hope. He wants to show that he can change things so drastically. It could also be a way for Madara to prove his own power. By being able to transform Naruto in such a radical way, he's demonstrating his control over powerful forces. And perhaps, in some strange way, he wants to see how Naruto would develop in a different form, out of sheer curiosity.
Madara might turn Naruto into a girl as a means of distraction. Naruto is a powerful opponent, and by changing his gender, it could divert his attention from his main goals. He'd have to deal with all the new aspects of being a girl. Also, it could be part of Madara's grand plan to reshape the ninja world. He might think that by changing someone as important as Naruto into a girl, he can influence the future of the ninja world in a different way. Maybe he believes that a female Naruto would make different decisions that would be more in line with his own goals.
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 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 reason could be for protection. Maybe Naruto is hiding his true identity from an enemy who is specifically targeting him. He might be using the mask as a disguise to blend in and gather information without being recognized.
Perhaps Kabuto wants to use Naruto as a pawn in his own schemes. He might think that by reviving Naruto, he can control the situation in the shinobi world to his advantage.
Maybe Itachi saw Naruto as a potential force for good in the ninja world. He might have thought that giving Naruto the Sharingan would make him strong enough to protect the village and bring peace.
One possible plot could be that Naruto, after being hit by a strange jutsu during a mission, turns into a little girl. His friends are initially shocked but then try to find a way to reverse it. Sakura might take on a big - sister role, protecting 'Naruko' from any potential threats while they search for a cure.
One possible plot could be that Sakura uses a new jutsu she's been working on accidentally and it turns Naruto into a girl. Naruto then has to deal with the sudden change, like how people in the village react differently to him/her. Maybe he/she has to learn new ways of fighting as a girl, with different physical abilities. And there could be some comical moments as Naruto tries to adapt to wearing girl's clothes and doing girl - like things.
Well, it could be part of a grander plan. Kami might know of a future threat that only a girl - Naruto can defeat. By turning Naruto into a girl, Kami is preparing him for this upcoming challenge. It could also be a test of Naruto's adaptability. Kami wants to see if Naruto can handle such a drastic change and still remain true to his ninja way. And perhaps there's some sort of prophecy or prediction that involves a female version of Naruto, so Kami is just making it happen to fulfill that prophecy.
One possible plot twist could be that Orochimaru turns Naruto into a girl as part of a grand experiment. But Naruto, now a girl, still has his (or rather her) strong will and uses this new form to infiltrate an all - female group that Orochimaru wants to target. This way, Naruto can gather intelligence and thwart Orochimaru's plans from the inside.
The Hidden Leaf Village would surely launch a rescue mission. They would send their best ninjas, like Sasuke, Kakashi, etc. This could lead to intense battles between Madara's forces and the Leaf Village ninjas. It would be a great opportunity to show off different ninja techniques and strategies.
In a 'Madara Adopts Naruto' fanfiction, perhaps Madara adopts Naruto because he sees a kindred spirit in him. Madara might want to mold Naruto into a powerful force to reshape the ninja world according to his own ideals. Naruto, on the other hand, could either resist or be influenced by Madara's views, leading to an internal struggle within Naruto as he tries to balance his own values with what Madara is teaching him.