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.
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.
Maybe it's a new villain in the fanfiction. Some powerful and evil character who sees Leo as a threat to their plans. This villain could use their unique powers or weapons to harm Leo. For example, a villain with the ability to control electricity could zap Leo and cause internal injuries.
It could be a jealous rival. This rival might be envious of Estel's popularity or skills and decides to harm her secretly.
It could be a rogue Death Eater who managed to catch Harry off - guard. Maybe they were lying in wait and launched a surprise attack when Harry was alone, away from the safety of Hogwarts.
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 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.
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.
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.
Perhaps it was a group of heroes working together. They combined their powers and strategies to get the better of All For One. Each hero might have contributed their unique abilities, like one hero using their speed to distract him while another used their strength to land a powerful blow, ultimately injuring him.