A possible plot development is that Nagato's act of helping Naruto causes a rift among the shinobi world. Some may see it as a threat while others may see it as a chance for a new era of peace. Nagato could also be the key to Naruto finally understanding the true nature of the tailed beasts and their connection to the Sage of Six Paths. This could lead to Naruto being able to communicate with all the tailed beasts more effectively and use their combined power in a new way.
In the fanfic, there could be a plot where Nagato helps Naruto in rebuilding Konoha. Nagato's power can be used for construction and restoration. He could also teach Naruto some of the secrets of the Uzumaki clan that he might have known, which would give Naruto an edge in future battles. And perhaps, Nagato's presence causes a shift in the political landscape of the ninja world as different villages react to their alliance.
One possible plot development is that Nagato and Naruto form an alliance to take on a new, greater threat. This threat could be an ancient evil that requires both Nagato's power and Naruto's spirit. Another development could be Nagato using his abilities to help Naruto unlock new powers or forms. For example, he might help Naruto better understand the Sage of Six Paths' power within him.
In these fanfics, Nagato may help Naruto on an ideological level. Nagato once believed in a very different way of achieving peace. By sharing his journey and how he came to realize the flaws in his thinking, he can guide Naruto in his pursuit of true peace. Nagato could also use his influence over the Akatsuki remnants to prevent them from causing more chaos, which in turn helps Naruto in his mission to protect the ninja world.
For Naruto, he would further develop his understanding and compassion. He would see that even the most seemingly evil characters have a backstory and reasons for their actions. This would make him even more determined to save everyone he can. For Tobi, his development would be huge. He could go from a revenge - driven, shadowy figure to someone who realizes the error of his ways and wants to make things right. He might learn about the value of life and friendship from Naruto.
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.
A plot development could be that Kakashi discovers the root cause of Naruto's neglect. It might be related to some hidden secrets in the village. Then Kakashi has to fight against those who are behind Naruto's neglect while still training Naruto. Another development could be that Naruto and Kakashi form a very strong bond. Naruto then uses the skills and confidence he gained from Kakashi to face his enemies and also to try and change the village's attitude towards him.
A possible plot development is that Naruto's study of chakra helps him master a new and powerful jutsu. For instance, he might develop a jutsu that can disrupt an opponent's chakra flow from a long distance. This would give him an edge in battles.
A third possible plot development could be the exploration of family values. Naruto, having grown up longing for a family, would be very committed to building a good family environment for Mordred. This could involve teaching Mordred about love, trust, and the importance of family bonds. Mordred, who may not have had such a positive family experience before, would then have to learn and grow in this new family setting. There could also be moments where Mordred has to defend Naruto or their family from external threats, which would strengthen their bond further.
One possible plot development could be Naruto leaving due to a misunderstanding. For example, if he is wrongly accused of a crime within the team. Another could be that he feels he is holding the team back in some way and decides to leave on his own to become stronger alone. Maybe he has a personal goal that he believes he can't achieve while still being part of Team 7.
One possible plot development could be that Naruto uses Kirin to surprise his enemies. Since it's not a jutsu associated with him usually, it would catch his foes off - guard.
One possible plot development could be the initial shock and adjustment for both Naruto and Mei. They would have to deal with the reactions of their respective villages. Naruto's friends in Konoha might be surprised, and Mei's allies in Kirigakure would also have their thoughts.
One possible plot development could be Naruto's ideals getting warped due to some traumatic event. For example, if he fails to save a dear friend, he might start to believe that the only way to achieve true peace is through extreme force. Another development could be his relationships turning sour. Maybe his friends start to fear his new, twisted self and Naruto, feeling betrayed, becomes even more deviated from his original self. Also, his view of the ninja world could change completely, seeing it as a place that needs to be remade in his own image rather than following the traditional ways.