In some stories, the merge might happen gradually. At first, Naruto starts having strange dreams about Dark Naruto. Then, he begins to notice small changes in his behavior and abilities. As the merge progresses, he has to learn to accept the parts of Dark Naruto that are now a part of him. His friends might be initially suspicious, but eventually, they come to realize that this new Naruto is still the same person at heart, just with a more complex set of powers and emotions.
Perhaps in the fanfiction, the merge between Naruto and Dark Naruto is caused by a powerful jutsu gone wrong. As a result, Naruto has to struggle to control the darker impulses while also harnessing the newfound power. This internal conflict could lead to some really engaging story arcs where he battles both external foes and his own inner demons.
One interesting plot could be the exploration of new powers that emerge when Naruto and Kaguya are merged. For example, perhaps a new form of chakra that combines Naruto's life - affirming energy with Kaguya's ancient and powerful chakra. Another plot might involve how the ninja world reacts to this new entity. Do they see it as a threat or a new source of hope? Also, the merged Naruto - Kaguya could have a unique perspective on the history and future of the ninja world, which could lead to revelations about hidden secrets or new ways to prevent future disasters.
There could also be some original characters created specifically for this fanfiction. For example, a powerful ninja who has knowledge about the merge process and tries to either help or hinder Naruto. Or perhaps an ancient spirit that was somehow involved in the creation of Dark Naruto in the first place and now has an interest in the merge.
Well, a plot might be that Dark Naruto in the fanfiction is on a journey to change the ninja world with his harem by his side. They could be facing off against the established shinobi villages' old ways. For example, they might try to create a new system where power is more equally distributed among all ninjas, not just the elite families. And the harem members could each have special skills that contribute to this goal.
One possible plot could be that Dark Naruto, with his newfound power and darker side, forms an unexpected alliance with Ino. Maybe they team up to take on a common enemy that the regular shinobi world is too afraid to face. In this story, Ino could use her mind - reading skills to help Dark Naruto control his rage and better understand his power.
In some naruto dark guild fanfiction, there might be a plot where the dark guild is secretly working with rogue ninjas to create chaos in the ninja world. They could be trying to disrupt the balance of power between the villages. For example, they might start false rumors about one village attacking another to incite war. This would force Naruto and his friends to not only deal with the physical threats but also the political unrest caused by the dark guild's actions.
One interesting plot could be the exploration of a darker side of the Naruto universe where the main characters face moral dilemmas they never had to in the original series. For example, Naruto might have to make tough choices between saving his friends and sacrificing his own principles in the 'dark empire' setting.
One interesting plot could be Naruto getting trapped in the SAO world and having to use his ninja skills in a virtual setting. For example, his shadow clone jutsu could be used in unique ways to overcome challenges in the game, like sending clones to explore different areas of the virtual world simultaneously.
One interesting plot could be where the neglected and dark Naruto is thrust into a crossover with another anime world, like Bleach. He could use his new - found darker powers to fight Hollows, and his experiences of being neglected could add depth to his character as he tries to find his place in this new world. Maybe he forms an unlikely alliance with a Soul Reaper who also has a troubled past.
Maybe Naruto gains new insights into the nature of chakra. The Kyuubi's chakra is very different from his own, and through the merge, he could understand how to manipulate chakra in ways he hadn't considered. This could lead to him teaching others new ways of using chakra as well.
In 'naruto dark naruto fanfiction', the concept of Naruto's doppelganger or 'dark Naruto' is often explored. This could be a manifestation of his repressed negative emotions. It might be that this dark Naruto has its own goals that are contrary to the real Naruto's. For instance, it could want to destroy the Hidden Leaf Village instead of protecting it. And the story could revolve around how Naruto deals with this inner darkness, either by trying to suppress it or, in a more extreme version, merging with it and becoming a different kind of hero or anti - hero.