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.
Another option is that it could be a new, unknown villain. This villain could have a grudge against the Hidden Leaf Village or Naruto specifically. They might have developed a unique ability that can directly attack Naruto's chakra core, causing it to overload and explode. Or they could be using some kind of forbidden art that has unforeseen consequences when used on Naruto.
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 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.
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.
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.
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 Danzo. He was always power - hungry and had his own ideas about what was best for the village. He might see Naruto as a threat and find a way to take away his birthright.
It could be a rogue ninja from another village who has a vendetta against Naruto. This ninja might have set a very elaborate trap that made it seem like Naruto was killed and left his body in a place where his friends would find him and think he was dead.