One possible plot development could be Naruto's friends rallying around him. They might seek out medical help, like Sakura using her skills to stabilize him at first. Then, they could start planning revenge against Pain. Another could be Naruto having some sort of vision during his injury, perhaps about his parents or a new power he could unlock to defeat Pain in the future. And, his sensei, Kakashi, could take on a more protective role over him as he recovers.
In the fanfiction, Naruto might struggle with self - doubt after being injured by Pain. He could question his strength and whether he's truly fit to be the one to bring peace. This internal struggle could lead to some character growth. Maybe he starts training in a new way, more focused on defense rather than just offense. Also, the villagers who once shunned him might start to see him in a new light, as a victim rather than just a powerful and sometimes feared force.
One possible plot development could be that her injury leads to a discovery of a new power within her. As she recovers, she realizes she can now do something she couldn't before, like communicate with a different species in the Shadowhunter world. This new ability then becomes crucial in the fight against a new threat that emerges.
One possible plot development could be that his friends, like Sakura and Sasuke, come to take care of him. Sakura uses her medical skills to try and bring down his fever. Another could be Naruto having fever-induced dreams about his past, like his lonely days as a child. Maybe he even hallucinates about his parents. It could also lead to a situation where the village is in danger, but Naruto is too sick to help at first, creating a sense of tension and urgency among the other characters.
One possible plot development could be Naruto finding strength within himself. He might start to question why his parents would do such a thing and through that self - reflection, he could begin to discover his own worth. Maybe he'll meet a mentor figure who helps him see that his parents' actions don't define him.
One possible plot development could be Naruto's struggle to break free from Orochimaru's control. He might have to face his inner demons and find new sources of power within himself. Another could be his friends trying to rescue him and having to fight against Orochimaru's minions. Maybe Naruto under Orochimaru's control is used to target the Hidden Leaf Village, creating a huge conflict.
One possible plot development could be Naruto developing new and unexpected powers as a result of the experiments. For example, he might gain the ability to use some of Madara's unique jutsu in a different way. Another could be Naruto's friends trying to rescue him and in the process learning more about Madara's true motives and the nature of the experiments. Maybe Naruto also has to struggle with his own identity as he is changed by the experiments.
One possible plot development could be Naruto focusing on rebuilding Konoha. He might use his newfound influence and power to inspire the villagers and make Konoha stronger than ever. Maybe he starts new training programs for the ninja of the village to better prepare them for future threats.
One possible plot development could be Naruto's internal struggle with the newfound power and responsibility. He might start to question his own limits and how to better protect the village in the future. Another could be the rebuilding of Konoha. Naruto could be deeply involved in the restoration efforts, both physically and mentally, trying to bring back the hope and strength to the villagers.
One possible plot development could be Naruto's efforts to rebuild Konoha. He might focus on strengthening the village's defenses and training new shinobi. Another could be his exploration of new jutsu, inspired by his battle with Pain. He could also work on improving relations with other villages.
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 possible plot development could be Naruto's struggle with the new responsibilities. After becoming Hokage, he might face challenges in rebuilding the village. He has to deal with the aftermath of Pain's attack, like repairing the damaged infrastructure and reassuring the villagers. Also, he might focus on improving relations with other villages to prevent future attacks. He could start new training programs for the younger generation to make the village stronger.