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.
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 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.
In some darker fanfictions, it could be a member of the Order who has always suspected Snape of being a double agent. This person might have decided to take matters into their own hands and attack Snape during the meeting, believing they are protecting the Order from a potential threat.
It could be Orochimaru. He's always been interested in experimenting on strong ninja. Naruto, being the main character, would be an interesting target for Orochimaru to mess with and cause this condition.
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 Sith or a Sith - inspired enemy. They are often the ones causing trouble for the Jedi, and shooting Ahsoka would be a way to strike at the Jedi Order.