Well, perhaps in this fanfic, there could be a betrayal within the village that Naruto fails to foresee. His friends or comrades turn against him due to some dark magic or mind control. As a result, he is caught off - guard and killed. It would be a very different and somewhat depressing spin on the Naruto we all know and love.
One possible plot could be that in a dark and alternate universe. Naruto might be facing an overwhelmingly powerful enemy that he simply can't defeat. Maybe an ancient evil has been unleashed and Naruto sacrifices himself to save the village. This would be a very tragic take on the Naruto story as he is usually seen as a symbol of hope and victory.
In this fanfic, it could be that Naruto is poisoned by a new and undetectable toxin. He gradually weakens and despite the efforts of Tsunade and the other medical ninjas, they are unable to find a cure. As he nears death, he reflects on his life and the dreams he had for the future of the village. His death would have a profound impact on the other characters, like Sasuke might be filled with regret for not being there for Naruto, and Hinata would be heartbroken.