In a Naruto becomes a master assassin fanfiction, the story might take a darker turn. Naruto could be forced into the role of an assassin due to some external threat to the Hidden Leaf. He might have to abandon his more open - combat ninja style and adapt to a more secretive and lethal approach. He would have to deal with the moral implications of taking lives, and perhaps struggle with his own identity as he transforms from a typical ninja into a feared assassin.
One possibility is that Naruto uses his shadow clone jutsu in a new and devious way for assassinations. He could send clones to gather intelligence, and when the time is right, he strikes with his signature rasengan in a stealthy manner. Maybe he would also learn new techniques from the world of assassins, like silent movement or poison use, all while still maintaining some of his ninja values like protecting his friends and village.
Well, the plot could involve Naruto being trained by a mysterious assassin figure. This person could teach him how to blend into the shadows, read his opponents' movements better. Naruto might start using kunai and shuriken more effectively for long - range kills. And his ability to transform, which he used for pranks before, could now be used to deceive his targets. For example, he could transform into an innocent bystander to get close to his enemy unnoticed.