The fanfiction could also be about a case of mistaken identity where someone else has been pretending to be Harry's father for some ulterior motive. As Harry digs deeper, he may find that this false father was involved in some dark plot all along. And Harry, being the hero he is, will have to use his skills and the help of his friends like Ron and Hermione to expose the truth and save the day.
In this fanfiction, perhaps there's a spell or some dark magic at play that has misled Harry all his life about his father. It could lead to a whole new adventure as he tries to find out the truth. He might have to face some old enemies of his real father or make new allies in the process of uncovering his true heritage.
Maybe the fanfiction could focus on Harry as a father dealing with the pressure of his kids being in different Hogwarts houses. For example, if one of his kids was sorted into Slytherin, he would have to overcome his own prejudices from his school days and support his child wholeheartedly. He could also teach them about the importance of unity between the houses.
In this fanfiction, it could start with an experiment in the magical research of both universes. Harry Potter, while exploring new magic, accidentally creates a portal to the world of Kotomine. Finding the young Kotomine in a difficult situation, Harry decides to stay and help him. As time passes, Harry imparts his knowledge of friendship, love, and the power of good magic to Kotomine. Their relationship grows, and they face various threats together, including enemies from both the Harry Potter and Fate universes who see their relationship as a threat to the established order. Harry's role as a father figure would be central to Kotomine's development, and they would embark on a journey of self - discovery and adventure.
One possible plot could be that a character, perhaps an unknown wizard, is revealed to be the 'Father of Monsters' in the Harry Potter universe. He could be creating new and dangerous creatures secretly, and Harry and his friends stumble upon this mystery during one of their adventures. Maybe these monsters are being used to disrupt the wizarding world's peace, and it's up to Harry to stop this 'Father of Monsters' and his evil plans.
A possible plot might involve the 'father of vampires' being a key figure in a prophecy that Harry discovers. The vampire has the power to either save or destroy the wizarding world. It turns out that he has his own motives and desires that are not entirely clear at first. He may be trying to gain control over the vampire population in the wizarding world, which has been growing out of control. Harry and his friends have to figure out whether to trust him or not as they try to prevent a war between wizards and vampires that could be catastrophic for both worlds. They also learn about the true origins of vampires in the Harry Potter universe through their interactions with the 'father of vampires'.
One possible plot could involve Harry Potter's father, James Potter, having some sort of encounter with a Murkrow (which is a Pokémon) in a fanfiction world where the boundaries between the Potterverse and Pokémon are blurred. Maybe the Murkrow has some special power or knowledge that James needs. As for Dokuro, if it's a character from a different series, it could be that this character is brought into the story as an ally or an enemy. For example, Dokuro could be a magical being from a different realm who tries to either help James achieve a goal or stop him from doing something dangerous.
It could be Sirius Black. Maybe there was some misinformation that made Harry believe Sirius was his father for a while, but then it turns out he isn't. After all, Sirius was very close to Harry and had a father - like relationship with him in some ways.
One possible plot could be that Loki, for some reason, was banished to the wizarding world long ago. He fell in love with a witch and had Harry. As Harry grows up, Loki reveals himself and starts training Harry in a more unorthodox form of magic. Along the way, they have to face the Ministry of Magic's suspicion as Loki's actions are often hard to understand. Also, they would have to deal with Voldemort, with Loki using his cunning to outwit the dark wizard.
Maybe in the fanfiction, there has been some sort of misunderstanding or false accusation that made people initially think Harry was the father. Then the story could be about him proving his innocence and finding out who the real father is.
The plot could involve a situation where a new form of dark magic is unleashed in the wizarding world, which spreads like wildfire and causes destruction similar to 911. The Ministry of Magic is caught off - guard. Hermione, with her vast knowledge, starts researching a way to counter this magic. Meanwhile, Ron and Harry lead the effort to protect the civilians. They set up shelters in places like the Room of Requirement and use Patronuses to guide people to safety. As they dig deeper, they discover that this dark magic was a planned attack by a long - hidden dark wizard group who wants to take over the wizarding world.
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.