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.
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.
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.
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.
One way could be through a magical portal. Imagine a portal opening between the Naruto universe and the Harry Potter world. Shisui, with his Sharingan abilities, could be a unique addition. His teleportation jutsu might be mistaken for a new form of Apparition in the wizarding world. Also, his skills in combat could be put to use in battles against dark wizards. For example, his ability to quickly assess and counter an opponent's moves would be very useful in duels at Hogwarts.
The poisoned apple could be a gift sent by a mysterious figure to one of the characters, like Iron Man. When he touches it, it starts to release a dark magic that affects his suit's technology. Harry Potter then detects the magic and tries to find a way to reverse the poison's effects.
In fanfiction, Mother Earth could be a hidden force that has been dormant for a long time. But due to some great imbalance in the wizarding world, she starts to awaken. Harry Potter might be the one to first sense her presence, maybe through a strange dream where he sees the earth itself calling out for help. Then, as the story progresses, he discovers that Mother Earth can communicate with certain wizards, and she imparts her wisdom to him to help him fight against the forces that are causing the imbalance, such as over - use of dark magic that is harming the natural world.
A pet could have unique powers that are useful in both worlds. Let's say a pet has the power of invisibility in the Harry Potter world. In the RWBY world, this power could be used to sneak up on Grimm or avoid detection by enemies. The pet could also form bonds with characters from both universes. For example, it could befriend Ruby and also get along with Harry, and through these relationships, bring the two groups of characters closer together.
Well, perhaps there's a special kind of magic in the far - flung corners of the wizarding world that allows for the creation of very unusual familiars. Harry, being the special wizard he is, might be drawn to this magic. The dinosaur could start as an egg that Harry discovers during one of his explorations. He then nurtures it with his magic, and as it hatches, it forms an instant bond with him. This dinosaur could have unique abilities that are useful in the wizarding world, like being able to sense dark magic from miles away or having the ability to camouflage itself in the Forbidden Forest.