One way is to create a crossover universe. Have Harry Potter's father be in a situation where he has to interact with a Murkrow, which could be a magical creature in this fanfiction rather than a Pokémon. Dokuro could be a character from a different dimension who is accidentally pulled into the Potterverse. They all then have to work together to solve a mystery that threatens all their worlds.
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.
One possible scenario in a fanfiction of Harry Potter's father and a Murkrow could be that the Murkrow is actually a transformed Animagus. James Potter might initially be suspicious of it but then realize it's an ally in some sort of secret mission against the Dark Arts. Since James was part of the Marauders, he was always into adventures, and this could be one such adventure involving a strange creature like the Murkrow.
Perhaps the Murkrow is a guardian of a hidden magical artifact. James Potter, being the adventurous type, tries to find this artifact. He has to first deal with the Murkrow, which is very protective. He could try to befriend it or use his magic to outwit it. In the process, we could learn more about James' character and his abilities as a wizard.
Well, in fanfiction, you could have Harry's magic interact with the Incredibles' superpowers in a fight. For instance, if they were facing a common enemy. Harry could use spells to enhance the Incredibles' powers. His levitation charm on Mr. Incredible could make him jump even higher and land more powerfully.
It can combine the two by having the characters cross over. For instance, Harry could be invited to MI6 to share his knowledge of dark magic as they face some sort of dark magical threat in the Muggle world.
A way to combine them in a father - son fanfic is to have the father and son be magically linked to both universes. Maybe they have a special ability that allows them to travel between the two. They could then introduce characters from one world to the other. For example, Gandalf could meet Dumbledore, and the father - son pair could be in the middle of this encounter, learning from both great wizards.
They could be in a time - travel scenario. Harry Potter accidentally takes Rose and Dobby back in time. They have to work together to get back to their own time. Dobby's house - elf magic might be crucial in finding a way back, while Rose uses her modern - day knowledge of magic (maybe she's read a lot about old magic) to help them along, and Harry Potter uses his experience from his own adventures.
They can combine in terms of magic systems. In some fanfictions, the powerful and often incomprehensible magic in the Cthulhu universe might blend with the more structured magic of Harry Potter. For example, a spell in Harry Potter might be corrupted by Cthulhu's influence and become a more dangerous and unpredictable force.
Their powers could combine in a really cool way. Harry's magic could enhance Starfire's energy blasts. For example, he could cast a spell on her hands that would make her energy blasts more powerful or more accurate. On the other hand, Starfire's superhuman strength could help Harry in physical combat situations. If they were surrounded by enemies, Starfire could use her strength to clear a path while Harry used his magic to hold off any attackers from a distance.
The settings are also combined. Hogwarts could be a place where some Twilight characters visit or even study. Imagine Bella trying to learn spells in Hogwarts, while also dealing with her attraction to Edward. It would be a whole new experience for her. And vice versa, vampires' lairs could be a place where Harry Potter characters end up, and they'd have to navigate the vampire world's rules.