A plot could revolve around Naruto and Nagato growing up together. Since they are cousins, they would have a natural connection. Nagato's experiences in the past might make him more cynical compared to Naruto. However, Naruto's unwavering belief in peace could start to influence Nagato. They could go on a journey to understand more about their family roots, and during this journey, they face various challenges that test their relationship and their own beliefs. Along the way, they might encounter characters who knew their family members and gain more insights into their family history. This could lead to a change in Nagato's perspective and ultimately, they could strive towards a common goal of bringing peace to their world.
Well, one possibility could be that Naruto discovers his relation to Nagato early on. This might lead to a whole different dynamic in the story. Maybe Nagato would be more hesitant to fight Naruto, and Naruto could try to understand Nagato's pain from a more personal perspective, instead of just seeing him as an enemy. It could also mean that Naruto has access to some of Nagato's knowledge or abilities in a unique way.
One possible plot could be that Nagato, seeing Naruto's potential and his kind heart, decides to take him under his wing. He could teach Naruto different jutsus and his unique view of the ninja world. This would change Naruto's growth path as he'd be influenced by Nagato's experiences and beliefs.
The plot could also explore how Naruto's identity as Nagato's son affects the Akatsuki. Maybe some members of the Akatsuki would try to recruit him or use him for their own purposes. On the other hand, Naruto might try to reform the Akatsuki from within. His connection to Nagato could also lead to a different resolution of the conflict between the ninja villages. Instead of just uniting the villages as in the original story, he could aim to create a more global peace based on Nagato's broader view of the world, which was not just limited to the ninja villages.
One plot idea could be that they discover their family connection early on. Maybe they find a hidden family tree or an old letter that reveals the truth. This could lead to them having to work together secretly to protect their newfound family bond from the wizarding world's prejudices.
Another plot could be that Nagato is reborn with new powers. With these powers, he aims to unite the different ninja villages in a more peaceful way than before. He could start by building alliances through diplomatic means and by using his powers to solve common problems, like natural disasters or threats from outside the ninja world.
Maybe Nagato had a relationship with an Uzumaki woman before he became fully involved in the Akatsuki. This woman could have given birth to Naruto but for some reason, Naruto was separated from Nagato at a young age. It could be due to the chaos and danger that Nagato was getting into with his plans for the Akatsuki.
One possible plot could be Nagato teaching Naruto his unique jutsu skills. Since Nagato has powerful abilities like the Rinnegan, he could pass on some of that knowledge to Naruto, which would make Naruto even stronger and give him new ways to fight enemies in the story.
One possible plot could be that Nagato and Konan, having had a change of heart after their past experiences, sense a great danger approaching Naruto. They use their unique abilities to fend off the enemies. Nagato with his Rinnegan powers could manipulate gravity and repel powerful attacks, while Konan, with her origami - like jutsu, creates barriers and distractions. Maybe they are trying to make up for their past wrongs by saving Naruto, who represents a new hope for the ninja world.
One possibility in fanfiction is that Nagato's sealing is a result of his own guilt. After realizing the extent of the destruction he has caused, he might allow himself to be sealed. This could be a very emotional and character - driven plot point. For example, he may feel that by being sealed, he can atone for his sins. And the story could then explore how the other characters react to this self - imposed seclusion of Nagato, and whether they try to convince him otherwise or accept his decision.
A plot could involve the challenges they face during the pregnancy. Maybe there are threats from old enemies who see the baby as a potential target. Naruto and Temari then have to take extra precautions to protect themselves and the unborn child. They could also go on a journey to find a special kind of medical ninja who can ensure a safe pregnancy for Temari, especially if there are some complications due to her being a ninja. Along the way, they might discover new things about each other and grow even closer as a couple.