Well, perhaps the main character, as a puppeter, could start a school or training ground for others interested in puppetry in the Naruto universe. This could attract all kinds of characters, both friends and foes. He might also develop a special bond with his puppets, almost like they are living beings, which could be a central theme in the fanfic. He could use his puppets to gather intelligence, as they can be sent into dangerous areas unnoticed.
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.
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.
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 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.
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 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 character development for Naruto is that he becomes more cautious. Kabuto has been a sly and unpredictable character. Meeting him might make Naruto less likely to trust so easily. On Kabuto's side, he could develop a sense of self - worth outside of being Orochimaru's subordinate. He might start to see himself as an individual with the potential to do good, and his character could transform from a somewhat villainous figure to an anti - hero or even a hero, depending on how the fanfic unfolds.
For Naruto, he could develop more patience and understanding. Usually he's quick to act, but being around Hana Inuzuka, he might learn to think things through more. Hana, on the other hand, could become more open - minded. She's from the Inuzuka clan which has its own set of traditions. Interacting with Naruto, who is quite different, could make her more accepting of new ideas. For example, Naruto's belief in never giving up on anyone could influence her to be more inclusive towards others in the village.
Naruto could become more in - touch with his animalistic side, which might initially make him seem more wild or unpredictable. But as he learns to control it, he could gain a new level of confidence and power.