Perhaps Naruto, as Orochimaru's apprentice, discovers some secrets about Orochimaru's past that make him more sympathetic towards him. This could lead to Naruto trying to redeem Orochimaru in some way. He might use his own positive influence to change Orochimaru's ways, which would be a major shift in the dynamic between them.
One possible plot development could be Naruto struggling with Orochimaru's dark teachings while still holding onto his own sense of justice. Maybe he tries to find a way to use Orochimaru's knowledge for good. For example, he could learn some unique jutsu from Orochimaru and then modify them to be less harmful or more in line with Konoha's values.
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 learning some of Orochimaru's unique jutsu. For example, he might pick up on Orochimaru's snake - related techniques. This could give Naruto an edge in combat against opponents who are not familiar with such unorthodox attacks. Also, Orochimaru's knowledge of forbidden jutsu might be passed on to Naruto in a modified, less dangerous way, which could then be used to surprise his enemies in future battles.
The apprentice could learn unique jutsu from Orochimaru. Since Orochimaru is known for his forbidden jutsu, the apprentice might gain an edge in combat but also face the danger of being corrupted by the power. They could then use these skills in battles against common enemies. And, in the process, they might try to redeem Orochimaru in some way, like showing him that there is a better path than his thirst for power.
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 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'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.
One possible plot twist could be Naruto struggling with the dark reputation associated with Orochimaru. Since Orochimaru is known for his unethical experiments and evil deeds, Naruto might face distrust from the village. Another twist could be that Naruto has an inborn talent for snake - related jutsus due to his supposed father. This could lead to a whole new set of training and challenges as he tries to master these unique abilities while also dealing with the moral implications of using Orochimaru - inspired techniques.
One possible plot twist could be that Orochimaru saves Naruto not out of pure kindness but for his own ulterior motives. Maybe he wants to use Naruto's power later for his experiments. Another could be that Orochimaru's save leads to Naruto having to make a difficult choice between his loyalty to the village and the debt he owes to Orochimaru. And perhaps Orochimaru's act of saving Naruto causes a rift between Naruto and some of his friends who don't trust Orochimaru.
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.