Maybe a group of radical villagers who fear Naruto's power as a jinchuriki. They could be so afraid of the potential destruction he could cause, even though Naruto has shown time and again that he is on their side, that they push for his execution.
It could be Danzo. He has always been a bit of a shadowy figure with his own motives in the Naruto series. He might see Naruto as a threat to his power and influence within the village and engineer a situation where Naruto is executed.
It could be the elders of the Hidden Leaf Village. They might see Naruto as a threat to their traditional way of ruling. For example, if Naruto starts to question their decisions too much or tries to bring about radical changes too quickly, they could conspire to have him executed.
It could be a new and powerful villain who has emerged. This villain might have a special ability that catches Naruto off - guard during a fight, leading to his injury.
It could be Orochimaru. He's always been interested in power and experimenting. Maybe he sees Naruto as a perfect guinea pig to test some new jutsu that goes horribly wrong and causes Naruto to explode.
Maybe some of the more conservative village elders. They have always been a bit wary of Naruto because of the Nine - Tails inside him. So they might be behind his capture in the fanfiction.
It could be Madara Uchiha. He was always seeking power and new ways to achieve his goals. Turning Naruto into a weapon would be a great advantage for him in his plans to reshape the ninja world.
It could be Orochimaru. He has always been interested in Naruto's power. Maybe he locked Naruto in a cage to study his chakra or to use him in some kind of dark experiment.
A new and powerful rogue ninja could be responsible. This ninja might have a vendetta against Konoha and see Naruto as a symbol of the village, so they target him and use their strong and devious techniques to injure him badly.
It could be the students. They might think Snape is too gloomy and old - fashioned in his appearance. So, as a bit of mischief or maybe out of kindness, they use their magic skills to give him a makeover. For example, Harry Potter and his friends could be behind it, using spells they learned in their Defense Against the Dark Arts class.
A rogue ninja from a rival village could be responsible. They might see Naruto as a threat and use their fire - based attacks to harm him. For instance, a ninja from the Hidden Mist Village who has a grudge against Konoha and targets Naruto specifically.
It could be Orochimaru. He's always been interested in Naruto's power, especially the Nine - Tails within him. He might have come up with a new devious plan to capture Naruto and use his power for his own dark experiments.