Well, it could be about Naruto being a huge fan of Ganondorf's power and trying to incorporate some of his dark and dominating traits into his own ninja style. Maybe Naruto starts to study Ganondorf's strategies and uses them in battles against tough opponents in the ninja world.
The fanfic could start with Naruto accidentally stumbling upon a portal that leads to a world where Ganondorf exists. Naruto is immediately in awe of Ganondorf's presence and strength. He decides to follow Ganondorf around and learn from him. Ganondorf, seeing Naruto's potential, decides to train him in a different way of combat. However, as Naruto spends more time with Ganondorf, he realizes that Ganondorf's motives are not always pure. This causes Naruto to have an internal struggle as he tries to take the good parts of what he has learned from Ganondorf and leave the bad parts behind.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Maybe Ganondorf adopts Fem Link in an attempt to break the cycle of their eternal struggle. He hopes to raise her to be different from the typical hero. As Fem Link grows, she discovers her true identity and has to grapple with her loyalty to Ganondorf, who has been like a father to her, and her destiny as the hero. Along the way, she might meet other characters from the Zelda universe who try to sway her in different directions.
Power is a very common theme. Since Ganondorf is often associated with his thirst for power, many fanfics explore how he obtains it, uses it, or loses it.
The story could start with her discovery of her true parentage. Maybe she's raised in the wizarding world as a normal witch, but then something happens that reveals she's Ganondorf's daughter. This could lead to her being ostracized or feared by some in the wizarding community. Meanwhile, she has to figure out how to control the dark powers that start to surface within her, all while trying to fit in at Hogwarts and deal with Voldemort's threat as well.
In a 'Naruto is the Raikage' fanfic, the plot could be that Naruto is transported to an alternate universe where he is the Raikage. He has to quickly adapt to the Cloud Village's culture and politics. He might face a powerful enemy that is targeting the Cloud Village specifically. Naruto then uses his experience from Konoha and his Uzumaki heritage to find a way to defeat the enemy. Meanwhile, he tries to bridge the gap between the different clans in the Cloud Village and bring about a new era of peace and prosperity. There could be a lot of sub - plots involving his relationships with the Cloud ninja, his attempts to improve the village's infrastructure, and his struggle to maintain his own identity while taking on this new role.
One possible plot could be that Naruto somehow gets transported to a world where Deathstroke exists or vice versa. Naruto then has to adapt to Deathstroke's way of fighting and living. He might face challenges where he has to use his new - found Deathstroke - like skills to survive against enemies he's not used to.
One possible plot could be Naruto using his scientific knowledge to improve the ninja world. For example, he might develop new jutsu that are based on scientific principles rather than just chakra manipulation. He could study the properties of different elements in a scientific way and create more powerful and efficient attacks.
In a 'naruto is nero fanfic', perhaps Naruto is mistaken for a powerful being in Nero's world. Nero might initially be cautious of Naruto but then realize they share a common goal of protecting the weak. They could team up to fight against a powerful dark force that threatens both their worlds, with Naruto using his Rasengan and Nero using his Devil Bringer in combination.
Well, if there was a 'naruto is vanitus fanfic', it could be about Naruto somehow inheriting the powers or characteristics of Vanitus. Maybe Naruto has to deal with the new - found powers and how they affect his relationships in the Naruto world, like with Sasuke and Sakura.
Maybe Naruto uses his rap skills to spread his ninja way. He could rap about his training, his friends, and his determination to become Hokage. His raps might inspire other characters in the Naruto universe.