In this kind of fanfiction, it might be justified by a complex web of alternate universes. Perhaps there's a universe where the laws of magic and detective work are intertwined. Harry Potter, with his skills and powers, could have entered a different dimension where he met someone related to Sherlock's family line. His actions there, whether intentional or not, could have led to the birth of Sherlock. Fanfiction often plays with these wild ideas.
Well, in fanfiction, the author can bend the rules of the original universes. Maybe it could be justified through some sort of time - traveling magic. For example, Sherlock could be from a future time where magic and Muggle worlds have merged in some strange way, and Harry Potter, through his powerful magic, was able to travel back in time and have a relationship that led to Sherlock being born. It's all about the creativity of the fanfiction writer.
Perhaps in this fanfiction, there is a hidden backstory where Grimmjow had an adventure in a world similar to Naruto's. He could have had a relationship with a woman there who had some sort of special power or connection. This relationship then led to the birth of Naruto. It might also be that some sort of genetic or magical experimentation was involved that combined their DNA in an unexpected way.
Yes, it's possible in fanfiction. It could be justified as self - defense. If a dementor was about to attack an innocent, especially someone Harry cared about, he might be pushed to use a powerful spell to kill it rather than just the Patronus charm which usually just drives them away.
Harry Potter can be seen as a superhero. He has powers that are unique to his world, magic. He uses these powers to protect his friends, Hogwarts, and the entire wizarding world from the forces of evil. Just like a superhero, he has a sense of justice and is willing to risk his life for the greater good.
In some fanfiction, the idea of Harry Potter being betrayed by his parents might be justified through a complex web of magic and prophecy. Maybe the parents thought sacrificing Harry was the only way to save the wizarding world from a greater evil. However, this goes against the essence of their characters in the original books.
One way is through the mystery - solving aspect. Harry and his friends often have to figure out what's going on in the wizarding world. Just like Sherlock Holmes, they gather clues, make deductions. For example, when they are trying to figure out the mystery of the Chamber of Secrets, they look for signs, ask around, and piece together information, much like Holmes would do in his cases.
One possible way is if Aphrodite, in the context of this fanfiction, represents a force that Naruto sees as having corrupted his family or his ninja way. Maybe Aphrodite's ideas about love and beauty conflict with the values Naruto has been taught in the ninja world, like loyalty and self - sacrifice. So he could develop a hatred towards her for what he perceives as her negative influence on his family.
One plotline could be Sherlock growing up with some sort of magical ability that he has to hide in the Muggle world. Since Harry Potter is his father, he might inherit some latent magic. He could use this in his detective work, like being able to sense when someone is lying in a way that's more than just normal intuition, because of his magical heritage.
One way it could be justified is through a dark magic plot. Maybe Voldemort uses some powerful and ancient magic to bind Hermione to him against her will at first. But as time goes on, she starts to understand his past traumas which led him to become so evil, and in a twisted way, tries to reform him. However, this goes completely against the original good - evil divide in the Harry Potter series.
In some fanfictions, it could be Sirius Black. Some fans like to imagine that Sirius had a deeper connection to James Potter's family than just being best friends. They might create a scenario where there was some sort of magic or prophecy involved that made Sirius more than just Harry's godfather, but his actual father in this alternate story line.
Perhaps a unique fanfiction would be one where Harry Potter, the Master of Death, has to hide his identity from the Muggle world while still helping Sherlock. He could use magic in very subtle ways that Sherlock starts to notice but can't quite figure out. This would create a lot of tension and mystery in the story, as Sherlock tries to solve the mystery of Harry's abilities while Harry is trying to keep his magic a secret.