One possible plotline could be exploring their shared heritage. Maybe they discover they are brothers early on and team up against the darker forces in the Naruto universe. They could use their combined powers to bring about a new era of peace in the shinobi world.
One possible plotline could be Naruto having to deal with the memories and powers of Madara suddenly awakening within him. He might struggle to control the dark and power - hungry side of Madara that comes with the reincarnation. This could lead to a conflict within the Leaf Village as they see Naruto changing.
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.
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.
One possible plotline could be that Madara kidnaps Sakura to use her as a bargaining chip against Naruto and the Hidden Leaf. Maybe he thinks her medical skills can be useful to heal his own troops or himself. Another could be that Madara has some strange fascination with Sakura's strength and potential, and wants to study her or turn her to his side.
One possible plotline could be Naruto facing unique challenges due to his Uchiha heritage. For example, he might have to deal with the stigma that the Uchiha clan had in the village, while also trying to live up to the legacy of Madara. Another could be that his Sharingan powers develop in a new and unexpected way, leading to new jutsu and abilities. Maybe he discovers some long - lost Uchiha secrets that give him an edge in battles against powerful foes.
Well, it might be that Rias sees Naruto as a rival in terms of power or influence in a new setting. So, she uses her devilish powers to abuse Naruto. In the story, Naruto could start out confused and hurt but then draw on his ninja training and positive relationships back home to slowly turn the tables and make Rias see the error of her ways. Maybe he even teaches her about friendship and loyalty, which are concepts not as prominent in her world.
Maybe the story focuses on Naruto learning about leadership from Hashirama. Hashirama was the first Hokage and had great leadership skills. He could teach Naruto how to make tough decisions for the good of the village, how to inspire the people, and how to deal with political situations within and outside the village.
Well, it could start with Anko being given false information about Naruto. Let's say someone convinces her that Naruto is secretly working with an old enemy of Konoha. She then starts to spy on Naruto. As she does this, she uncovers some things that seem to confirm the false information, but in reality, they are just coincidences or set - ups. So, she feels she has no choice but to betray Naruto to protect the village. It could also be that Anko has her own ambitions that conflict with Naruto's goals for the village, and she sees betraying him as a way to achieve her own ends.
One possible plotline could be Naruto discovering his connection to Madara later in his life. This revelation could send shockwaves through the ninja world. Maybe he'd face discrimination or extreme reverence because of it. Another could be that Naruto has some latent powers inherited from Madara that start to emerge and he has to learn to control them while also dealing with the political implications of being related to such a controversial figure.
One possible plotline could be that Madara's great - grandson discovers a hidden power within himself. Maybe he finds an ancient scroll left by Madara that contains a unique jutsu. He then has to train hard to master this jutsu while also facing off against new enemies who want the power for themselves.