One way could be to make Naruto and his friends into SCP - like characters. Naruto's ability to use chakra could be seen as an anomalous power that needs to be studied and contained. The Leaf Village could be like a Foundation site, and they have to deal with other villages as if they were other 'threats' in the SCP universe. For example, Orochimaru could be a more menacing and SCP - style villain, with his experiments being even more grotesque and dangerous.
Well, the story could start by reimagining the origin of Naruto. Maybe he was created as an SCP - like experiment. His Nine - Tails power could be something that the SCP Foundation would be extremely interested in. As the story progresses, the other characters like Sasuke and Sakura could be drawn into this new SCP - Naruto world. They could be tasked with either helping Naruto control his 'anomaly' or having to face the consequences if he loses control. There could also be crossovers with other SCP elements, like having SCP - related artifacts appear in the Naruto world and causing chaos.
One way could be to give Harry the Geass power. So, he could use it to control the actions of Death Eaters or Voldemort himself. He might start to make more strategic and calculated moves like Lelouch, using his new power to outwit his enemies. Another aspect could be in the political side. Maybe the wizarding world becomes more like Lelouch's world with different factions vying for power and Harry has to play a political game as well as fight against the dark forces.
The plot could start with Harry having strange dreams about Shinigami. As he investigates, he discovers that there is a hidden portal in Hogwarts that leads to a realm where Shinigami exist. He and his friends enter this realm, and they find out that there is a dark force in the wizarding world that is related to the Shinigami in some way. They then have to work with some friendly Shinigami to stop this dark force. Along the way, they learn about new forms of magic and the true nature of death from the Shinigami.
The plot could start with a spell gone wrong in Hogwarts that somehow transports a group of Transformers to the wizarding world. The wizards are initially scared but soon realize that they need to cooperate with the Transformers to deal with a new dark force that is attracted to the combination of magic and technology. The story could involve battles, magic - tech hybrids, and new friendships between the two groups.
One way could be to have Harry be adopted by a Mandalorian family. He grows up learning both magic and Mandalorian combat skills. Then, he has to use his combined knowledge to fight against a common enemy that threatens both the wizarding world and Mandalore.
One way the story could be developed is by showing Naruto's reasons for becoming a pickpocketer. Maybe he's desperate to help his village in some way and sees pickpocketing as a quick solution. For example, he could be stealing from the rich to give to the poor in Konoha. This would add a Robin - Hood - like aspect to the story.
If Naruto becomes a Pokemon fanfiction, it could go like this. Naruto, being his curious self, would be intrigued by the concept of Pokemon. He might meet some Pokemon trainers who teach him the ropes. His natural leadership skills would help him in leading his Pokemon team. He could also bring some of his ninja tools and incorporate them into his Pokemon training and battles. For instance, using his kunai to mark the location of wild Pokemon. His journey would be filled with new adventures, making friends with other trainers, and learning about the different regions in the Pokemon world.
One way could be through Naruto's admiration for Kisuke's unique skills. Maybe Naruto discovers Kisuke's swordsmanship or his knowledge of spiritual energy. He then starts to study Kisuke's ways, trying to incorporate some of his techniques into his own fighting style. This would lead to Naruto changing his combat approach and even his way of thinking about battles.
One way the story could be developed is that Naruto's death could trigger a chain of events within the Hidden Leaf Village. His friends, like Sasuke, might be filled with guilt and anger. Sasuke could vow to avenge Naruto and start a dark path of seeking extreme power. Meanwhile, the village would be in mourning, and the younger generation would see Naruto as a martyr, inspiring them to train harder to protect the village in his memory.
In the fanfiction, their love story could be set in a new world where both Naruto's and Rias' universes collide. Maybe Naruto is on a mission in Rias' world and they meet by chance. Naruto's unique powers like the Rasengan would be a novelty in Rias' world, and she would be intrigued. As they get to know each other, they start to care for one another, and love blossoms. It could also involve some cultural exchanges between the two different settings.
One way could be through some sort of magical or cross - dimensional event. Maybe a powerful magic user or a godly artifact messes up the fabric of different mythologies and universes, bringing Naruto and Aphrodite together. Naruto, with his strong sense of loyalty and justice, might initially be very confused by Aphrodite's beauty and the concept of Greek gods.