One common theme could be mystery. Given the nature of the characters, there might be elements of an unknown backstory or a hidden connection between them that the fanfic explores. Another theme could be redemption, perhaps the purple guy trying to make up for his actions in relation to the puppet.
I'm not entirely sure if there is a specific, well - known fanfiction where Naruto is a human puppet. However, given the vastness of the fanfiction community, it's very possible. Fanfictions can range from the most outlandish to the more subtle in their changes to the source material. This idea of Naruto as a human puppet could potentially be used to tell a very dark or a very different kind of story about him.
A Naruto living puppet fanfiction often explores unique concepts. It could involve a character creating living puppets in the Naruto universe. Maybe a rogue ninja discovers a new jutsu to bring puppets to life and uses them for various purposes, like creating an army or for espionage.
One popular theme is the transformation of traditional puppets into living entities. This can bring a whole new level of combat and strategy to the Naruto story. Another theme could be the relationship between the puppet master and the living puppet, which might be more complex than with regular puppets.
I'm not sure about specific 'purple guy x puppet fanfic' stories as it's a rather niche and often fan - created content. You could try searching on fan - fiction platforms like Archive of Our Own. They might have some works related to this pairing if it exists within the relevant fandom.
One possibility is that Naruto could use his new puppet - making skills to create unique puppets inspired by his friends. For example, a puppet modeled after Sasuke with some of his signature moves. Another aspect could be how he combines his ninjutsu with puppet control. He might infuse his Rasengan into a puppet for a powerful attack.
Typically, in such fanfiction, Naruto is likely to be at the center of the story. The 'puppet' aspect might involve characters related to the puppet - using techniques in Naruto, like Kankuro perhaps. The 'harem' part means there will be multiple characters, usually female, having some sort of relationship with Naruto. It could be romantic, or they might be allies in a unique way.
One interesting 'Naruto Puppet Master Fanfic' could be 'The Puppeteer's Ascent'. It focuses on a character who discovers their unique puppet - making abilities and how they use it to gain power in the Naruto universe. They start from being an outcast and gradually rise in status.
One common theme is the power of the puppets. Fanfictions often explore how powerful a puppet master can be with their creations. Another theme is the mystery behind the art of puppetry. It could be about the secrets of making unique puppets or controlling them in special ways. Also, the relationship between the puppet master and their puppets is a frequent theme, like whether they see them as just tools or something more.
There's a possibility that the Dark Puppet Master is a new character entirely, created specifically for the fanfic. This character could be from a small, unknown village that was destroyed by the larger ninja villages in a past war. Driven by revenge, they developed their puppet - controlling skills in secret and now emerge as a powerful and menacing figure in the Naruto fanfic.