It could be a new character entirely. Maybe a rogue ninja from a long - forgotten clan who holds a grudge against Naruto for some past event. This villain could be extremely powerful in dark jutsu and sees Naruto's death as the first step in his plan to take over the ninja world.
Perhaps an old enemy from Naruto's past that was thought to be defeated but actually managed to survive and regain strength. This villain might have a vendetta against Naruto for imprisoning him or causing the downfall of his organization. After Naruto's death, this villain could target Boruto, seeing him as a symbol of Naruto's legacy and wanting to break the will of the Hidden Leaf Village.
There is also a possibility that the main villain is a corrupted version of one of Naruto's friends or allies. This could be due to some dark influence or a tragic event that twists their mind. They could be the one responsible for Naruto's death, either directly or indirectly, and then become the main threat that Boruto has to face in the fanfiction.
It could be an unknown, ancient evil that has been awakened. This villain might have powers far beyond what Naruto and Sasuke have faced before. Maybe it's an entity from a forgotten era that was sealed away long ago and now has broken free.
One possible plot could be that Naruto sacrifices himself to save Boruto from a powerful new enemy. Maybe an ancient evil resurfaces that is too strong for Boruto to handle alone, and Naruto steps in, using up all his chakra and ultimately dying in the process.
One possible plot could be that Naruto sacrifices himself to protect Boruto from a powerful new enemy. Maybe an ancient evil has been awakened and Boruto is in its direct path. Naruto, being the hero he is, steps in and uses all his power to stop it. His death then becomes a catalyst for Boruto's growth, driving him to become stronger and more determined to protect the village in Naruto's memory.
It could be a resurrected Orochimaru. He has always had an interest in power and the Akatsuki. He might return, more powerful than ever, and take control of the Akatsuki in the Boruto era, using them to carry out his evil plans, like creating an army of super - ninjas using some dark jutsu.
It could be Doctor Doom. He might be seeking to take over multiple universes in a crossover. Spider Man stands in his way, and Doom, with his superior intellect and powerful magic, manages to defeat Spider Man. His death would then be a huge shock to other heroes in the crossover, like the Avengers or the Fantastic Four who then have to avenge him.
It could be a new dark wizard who has infiltrated Hogwarts under the guise of a new teacher. This wizard might have a vendetta against Harry specifically and sets up elaborate traps to kill him.
Perhaps there's a prophecy involved. The fanfic could be set up where it's foretold that Boruto will bring about a great change, but only if he survives a certain threat. Naruto, aware of this, sacrifices himself to ensure Boruto lives on. This could then trigger a series of events where Boruto has to deal with the political fallout in the village, as some may blame him for Naruto's death, while others see him as the key to the future. It could also lead to a rift between Boruto and some of his friends who struggle to understand why Naruto had to die for him.
In the 'naruto dies boruto fanfic', it could be that Naruto is killed by an unexpected betrayal within the village. This shatters Boruto's world. He then goes on a journey to find out the truth behind the betrayal. Along the way, he meets some of Naruto's old friends who help him train and grow stronger. Boruto also starts to uncover secrets about the village's past that his father was trying to protect, and he realizes he has to be the one to expose these secrets and bring justice to his father's death.
It could be a new character created just for the fanfiction. Maybe a rogue ninja who has mastered a dark and powerful jutsu that Naruto has no defense against. This antagonist could be seeking revenge on Konoha for some past wrong and sees Naruto as the biggest threat to his plans.
It could be someone who was secretly behind Naruto's death in the first place. Maybe a rogue ninja who has a vendetta against the Hidden Leaf and saw Naruto as a major obstacle.