It could be a rogue ninja from a neighboring village. Maybe they were hired by a shadowy organization that wanted to disrupt the balance of power. This ninja might have been specifically targeting Naruto because of his status as a hero and a symbol of hope for the Hidden Leaf Village.
It could also be a new, mysterious enemy that has emerged with a vendetta against Naruto specifically. This enemy might have some sort of past connection to Naruto that we don't know about yet in the fanfiction. They could have been biding their time and finally struck when Naruto was on this fateful mission.
It could be a powerful Hollows or Arrancar. Since they are often the antagonists in the Bleach universe, they might see Naruto as an intruder or a threat to their plans. Maybe a powerful Hollow with a thirst for powerful souls targets Naruto, thinking his unique chakra would be a great addition to its power.
It could be an old enemy seeking revenge. Maybe a powerful Titan who escaped Tartarus and blames Percy for his previous defeat. This Titan could have been plotting in secret, waiting for the perfect moment to strike and finally end Percy's life.
It could be an enemy ninja from another village who wants to take out Konoha's strongest shinobi. Maybe someone from the Sound Village still holding a grudge against Naruto.
A new organization that is bent on world domination could be the main antagonist. They set a trap during Naruto's mission. This organization might have access to some ancient and forbidden jutsu that they use against Naruto. They see Naruto as a major threat to their plans, so they target him specifically.
It could be a jealous student. Maybe someone who has a crush on the same person Harry is attracted to in the story. They see Harry as a rival and figure that by poisoning him with a love potion, they can make him look foolish or get him into trouble.
Maybe it's a new villain who is trying to make a name for themselves. This villain could see shooting Captain America as a way to gain instant notoriety in the criminal underworld. They might have studied Captain America's weaknesses and found an opportune moment to strike.
One way the story could be developed is that Naruto's death could trigger a chain of events within the Hidden Leaf Village. His friends, like Sasuke, might be filled with guilt and anger. Sasuke could vow to avenge Naruto and start a dark path of seeking extreme power. Meanwhile, the village would be in mourning, and the younger generation would see Naruto as a martyr, inspiring them to train harder to protect the village in his memory.
One possible plotline could be that Naruto is on a highly dangerous mission alone, perhaps against an extremely powerful and unexpected enemy. He might sacrifice himself to protect his village or his comrades. For example, he could be facing a new type of jinchuriki whose power he underestimated, and in the end, he uses all his strength to seal the enemy away, but at the cost of his own life.
It could also be a secret organization within the Naruto universe that we don't know much about in the original story. This organization might be aware of some hidden prophecy or potential in Naruto related to the Nine - Tailed Fox. They kidnap him with the intention of either preventing that potential from being realized (if they see it as a threat) or using it for their own mysterious ends.
Sasuke could be a likely candidate in a sense. Given his skills as a ninja, his Sharingan which gives him an edge in combat and perception, and his past as a sort of 'rogue' ninja. He could be in a situation where Naruto has to hire him for a special mission that requires his unique abilities. Another possibility is Kakashi. He has a vast array of skills, is very intelligent, and could easily take on the role of an assassin if needed, even if it goes against his normal moral code slightly. He would do it for Naruto's sake.