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 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.
Well, it could be about Naruto somehow losing control of his chakra in a new and extreme way that causes him to literally explode. Maybe an enemy uses a new type of jutsu that backfires on Naruto's own chakra system.
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.
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 was always interested in powerful jutsu and having Naruto, who is the Jinchuriki of the Nine - Tails, under his control would be a great asset. He might have planned a secret mission to snatch Naruto at birth for his experiments.
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 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.
Sasuke could be responsible. Their relationship has always been complex. Maybe in this fanfiction, their rivalry escalates to a point where Sasuke accidentally kills Naruto during a fight at the Valley of the End.