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.
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.
It could be a rogue ninja from another village who has a vendetta against Konoha. This ninja might have a special ability to target Naruto specifically and put him in a critical state.
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.
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.
The village elders are likely candidates. They are often shown to be power - hungry and manipulative in the Naruto series. They might see Naruto's power as a threat to their control over Konoha and thus plot against him, which could lead to Naruto feeling betrayed.
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.