Well, in such a fanfic, a plotline might involve Naruto's friends trying to rescue him. They could discover Orochimaru's lair where Naruto is being experimented on. Meanwhile, Naruto himself could be developing new and unexpected powers as a result of the experiments, which he then has to learn to control. And there could be a race against time for Naruto's friends to reach him before Orochimaru's experiments cause irreversible damage.
His character could develop in a darker direction. The torture and manipulation from Orochimaru's experiments could make him question his values. However, it could also strengthen his resolve to protect his friends and the village. He may start to see the world in a more complex way, understanding that there are greater evils out there. And his newfound powers from the experiments could give him a sense of responsibility that he didn't have before.
Naruto could develop a new sense of determination. He might be determined to not let Orochimaru's experiments define him. Instead, he could use what has happened as a motivation to become stronger in his own way. He may also start to study more about the type of experiments Orochimaru was doing, not to replicate them, but to find ways to counter any future threats related to that kind of science.
Well, Orochimaru is a very ambitious and somewhat deranged character. His motives for experimenting on Naruto could be multi - faceted. Firstly, he's always been obsessed with the Sharingan and other powerful kekkei genkai. Naruto, with his own powerful chakra source, might be a step in his research to create something that can rival or even surpass the power of the Sharingan. Secondly, Orochimaru is known for his experiments on humans to enhance their combat abilities. Naruto's natural strength and growth potential could be used to develop new combat - enhancing techniques that Orochimaru could then use for his own purposes, like building a more powerful army or just to satisfy his own scientific curiosity.
He survives through his strong will. Naruto has an unwavering determination that refuses to be broken by Orochimaru's experiments. His inner strength and the chakra of the Nine - Tails within him might also play a role in withstanding the physical and mental torture of the experiments.
Well, Naruto's friends would be in an uproar. Iruka, who has always been like a father figure to Naruto, would be heartbroken and would not rest until he knew Naruto was safe. The other Konoha ninja would also be affected. Neji, despite his initial coldness towards Naruto, has come to respect him. He would see Orochimaru's actions as a threat to the village and to his friend. Tenten would offer her weapon - related skills to help in any rescue attempt. And Hinata, who has deep feelings for Naruto, would be extremely distraught. She might even try to take on Orochimaru herself in a desperate attempt to save Naruto, regardless of the danger to her own life.
Perhaps Naruto starts to have a connection to Orochimaru's other experiments or creations. He might find himself in a situation where he has to either help or fight these other 'products' of Orochimaru's mad science. Also, the fanfiction could explore how Naruto's friends react to what has happened to him. Do they trust him still? Or are they afraid of what Orochimaru might have turned him into?
He could have physical deformities. Orochimaru's experiments are often extreme and might cause Naruto's body to change in abnormal ways. Also, he might have mental trauma. The experience of being experimented on could leave him with psychological scars that affect his relationships and his ability to trust.
In some fanfics, Naruto might use his new and powerful jutsu that he has mastered over time. Maybe he combines his Sage Mode with the power of the Nine - Tails in a unique way that Orochimaru can't counter. For example, he could use the Nine - Tails' chakra to enhance the range and power of his Sage Mode attacks, and then catch Orochimaru off - guard.
One consequence could be a shift in the power balance among the ninja villages. Since Orochimaru was a powerful and feared figure, his death might cause some chaos as his former allies or subordinates try to either avenge him or claim his resources. For example, some of his secret labs and experiments might be up for grabs, leading to potential conflicts.