One possibility is that the experiment goes wrong at first. Naruto might find himself in a situation where his body starts to reject the changes. However, through his determination, he could then figure out a way to overcome this and turn the experiment into a success. For example, if he was experimenting with a new form of Sage Mode, initially it could make him very ill, but later he could master it and gain new abilities like sensing enemies from much farther distances and having stronger physical attacks.
Well, he could gain some new and unexpected powers. Maybe he discovers a way to enhance his chakra control to an extreme level, allowing him to perform jutsus with much greater efficiency and power.
Well, it's possible that in the fanfiction, Naruto is experimented on as part of a desperate attempt to save the village. There could be a new threat on the horizon, and the village elders or some ninja with knowledge of forbidden techniques believe that by experimenting on Naruto, who has shown great resilience, they can find a solution. They might be trying to turn him into a weapon or a shield for the village, which would put Naruto in a really tough situation both physically and morally.
One possible plot could be Naruto developing new and unexpected powers as a result of the experiments. Maybe he has to struggle to control these new abilities while also dealing with his feelings of betrayal towards the village that allowed Danzo to do this to him.
The plot could take a dark turn. Naruto's friends might become worried about him and try to stop his self - experimentation. This could lead to a conflict between Naruto's desire for power and his friends' concern for his well - being.
In such a fanfiction, one possible scenario could be that Naruto is experimented on for his unique chakra. Maybe Konoha scientists, in a bid to understand the power of the Nine - Tails within him, conduct various tests that are both physically and mentally taxing for Naruto.
One possible outcome could be Naruto winning through his unwavering determination and newfound powers. He might use his Sage Mode combined with the power of the Nine - Tails to outwit the Ten - Tails.
One possible motive could be power. Danzo was always obsessed with having power in Konoha. By experimenting on Naruto, who is the Jinchuriki of the Nine - Tails, he might have hoped to harness the power of the Tailed Beast in some way. Maybe he thought he could create a super - soldier or gain some unique abilities from Naruto's connection to the Nine - Tails.
There are several reasons. He might be afraid of getting too close to people because he's lost someone important and is scared of more loss. It could also be that he's discovered some new power within himself that he doesn't understand and is worried about hurting others if he gets too involved. Additionally, there could be some political intrigue in the village. Maybe there are some people who are plotting against him and he's keeping to himself to avoid being a target or putting others in danger.
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?
Madara could be experimenting on Naruto to understand the concept of the 'will of fire' that Naruto embodies. Madara has his own views on power and the ninja world, and Naruto's unwavering belief in the will of fire might be something he wants to dissect. He may think that by understanding what makes Naruto so strong in terms of his beliefs, he can either break that strength or use it to manipulate others. Also, Naruto is seen as a symbol of hope in the ninja world, and Madara might want to turn that symbol into something that represents his own ideals through these experiments.
Perhaps the experiments by Cadmus would change Naruto in unexpected ways. His powers could be altered, and he might develop new abilities or lose some of his old ones. This could lead to a conflict within Naruto as he tries to come to terms with these changes. His friends in Konoha might initially be suspicious of him due to his altered state. But Naruto would strive to prove that he's still the same person at heart and use his newfound or remaining powers to protect his village from any threats related to Cadmus.