Even some of the village elders might be to blame in this fanfic. If they have some secret motives and see Naruto as a threat rather than an asset, they could manipulate situations in a way that endangers Naruto's life and eventually causes his death.
The villagers themselves could be responsible. Their constant ostracization and negative treatment of Naruto could lead to his downfall. He might be pushed to a point where he takes risks that ultimately cost him his life.
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.
One possible scenario could be that he succumbs to the hardships in the village as a child. Maybe the villagers' hatred towards him is too much to bear, and he gets into a situation where he can't defend himself. Another could be that he's on a mission early on and it goes horribly wrong, perhaps facing an enemy far too powerful for his young self.
In some versions, it could be a former ally who has been corrupted. This character, once on Ahsoka's side, has now turned against her due to some external influence or personal greed. Their knowledge of Ahsoka's strengths and weaknesses would make them a formidable opponent, and they could be the one to cause her death.
An unexpected character could be responsible. Maybe a character that Harry thought was harmless but was secretly envious of him. This character could have used some form of emotional manipulation, constantly undermining Harry's confidence and self - worth until his heart was broken and he died.
Perhaps an old enemy from Snape's past, someone who has a long - standing grudge against him. This person could have tracked him down to the Shrieking Shack and finally got their revenge. It could be someone related to his days as a Death Eater or even from his school days when he might have made some enemies.
Perhaps a member of the Justice League, accidentally. For instance, during a fight where powers go out of control. Let's say Flash runs too fast and accidentally knocks Batman into a sharp object, causing a fatal injury. This would create a huge moral dilemma within the League.
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.
The child could be an orphan from a small, destroyed village that Naruto comes across during one of his missions. This child might have lost their family to a powerful enemy and Naruto feels a sense of responsibility to take them in.
It could be Death Eaters. They are always on the hunt for Harry and his friends. If they manage to find Shell Cottage, they might see Hermione as a major threat and use a deadly spell on her.
Perhaps Gohan's own overconfidence could lead to his death. He might underestimate an enemy's power or a dangerous situation and make a wrong move that results in his end. For example, he could rush into a fight without proper preparation thinking he can handle it easily.