A plot could be that the cancer is a result of some sort of chakra - related experiment gone wrong in his past. Naruto initially brushes off the symptoms as just being tired from his work. But when it becomes clear it's something more serious, he has to come to terms with his mortality. His friends like Sasuke would be in denial at first, trying to find ways to save him against all odds. The story could end with Naruto's death being a catalyst for the village to make changes in how they handle ninja health and safety.
In a fanfiction with Naruto dying from cancer, the story might focus on how the ninja world reacts. His allies from different villages might come together to try and find a cure. However, Naruto, knowing the slim chances, might start to prepare for his death. He could pass on his teachings and the will of fire to the next generation in a more urgent and poignant way. His death could also lead to a shift in the power dynamics among the villages, as he was a unifying figure.