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.
A Murkrow could be a link to an otherworldly dimension. James Potter discovers the Murkrow while exploring a strange part of the wizarding world. The Murkrow could lead him to this dimension where there are new forms of magic and threats. James would then have to rely on his wits and the little knowledge he has to survive and come back, and this adventure could shape his future actions in the fight against the Dark Arts.
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.
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 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.
In fanfiction, the gun could be a magical - Muggle hybrid weapon. It could have been created by a wizard who was fascinated by Muggle technology. Harry gets hold of it, and it has unique properties. For example, it could fire spells instead of bullets, or the bullets could be enchanted to have special effects. This would blend the two worlds of magic and Muggle - ness in an exciting new way.
Daphne could be a researcher of ancient magical artifacts and she comes across some information about the Elder Wand that she shares with Harry. For instance, she might have found a dusty old book in the library that details a secret property of the wand. This information could be crucial for Harry in his journey regarding the wand.
One way could be through a crossover spell. Maybe a powerful dark wizard in the Harry Potter universe discovers a way to create a Rinnegan - like power. They might use it to gain ultimate control over magic, similar to how the Rinnegan gives great power in Naruto. This could lead to a new kind of threat that Harry and his friends have to face.
One way could be through a magical spell gone wrong. Maybe a spell that was meant to transform an object into a helper, like in Beauty and the Beast, but instead it affects a character in the Harry Potter universe in a similar way. For example, a student might be turned into a beast - like form and only the love of another can break the spell, much like in the original Beauty and the Beast story.
Venom's ability to heal quickly could also play an important role. In the Harry Potter series, injuries are common during battles and duels. A character with Venom's healing factor would have an advantage. They could survive attacks that would normally be fatal and keep on fighting. This could change the dynamics of battles in the fanfiction world. For example, if Harry was bonded with Venom, he could survive Voldemort's Killing Curse due to Venom's healing ability.
The Infinity Stones could be linked to the Deathly Hallows. Maybe the Resurrection Stone has a connection to the Soul Stone. They could both have the power over life and death in different ways. And the other Infinity Stones could be related to the Elder Wand's power of domination and the Cloak of Invisibility's power to conceal, but on a much grander scale, if they were to be incorporated into the Harry Potter world.
One way could be through a powerful ancient magic spell. A wizard discovers an old, forgotten spell that can summon and bind a Nemean Lion as a familiar. This spell might be hidden in a lost grimoire in a dusty corner of the Hogwarts library.