To integrate a Dark Puppeteer, you could explore their relationship with the existing elements in the Naruto world. Maybe they are descendants of an ancient puppeteer clan that was shunned and now they want to prove their worth by causing chaos. Their story could be intertwined with the history of puppetry in the Naruto universe, and their actions could lead to new revelations about the art of puppetry and its potential for good or evil.
A Dark Puppeteer could be part of a larger conspiracy in the Naruto fanfiction. They might be working with other villains to bring down the ninja villages. Their puppetry skills could be used to gather intelligence by controlling small animals or insects as puppets and spying on the villages. They could also create powerful puppet soldiers that are difficult for the regular ninja to defeat.
One way to integrate a Dark Puppeteer into Naruto fanfiction storylines is to make them a threat to the main characters. For example, they could target Naruto and his friends, using their puppetry skills to set traps or manipulate other characters into attacking them.