In such a fanfiction, perhaps Harry Potter could use magic to communicate with the aliens. For example, he might use a spell to translate their strange languages.
Well, it could be that the aliens are attracted to Hogwarts because of its powerful magic. They might come to learn magic from the wizards and witches there. And Harry Potter would be in the middle of all this, trying to figure out if the aliens have good intentions or not. There could be a whole adventure where they team up to fight a common enemy, like a dark wizard who wants to use the aliens' advanced technology for evil purposes.
One possibility is that the aliens' technology could interact in unexpected ways with the magic in the Harry Potter universe. Maybe their spaceships disrupt the magic fields around Hogwarts, causing all sorts of chaos. Harry Potter, being the hero, would have to find a way to restore balance. He might also discover that the aliens have a form of magic in their own world, and they exchange knowledge about different types of magic and technology.
Well, it could be that the Queen, being a symbol of order in the Muggle world, has to deal with the sudden appearance of Harry Potter and the chaos that magic can bring. Maybe she initially mistakes his magic for some sort of advanced technology and there are a series of misunderstandings that lead to an interesting adventure. Harry could introduce her to the concept of Hogwarts and she might be fascinated by the idea of a school for magic.
Well, one possibility is that the magic from the Harry Potter world and the chakra-based abilities in Naruto could combine in interesting ways. For example, a wizard might learn to use chakra to enhance their magic spells, or a ninja could use a magic spell to give them an edge in combat. Another idea could be that the characters from both universes team up to fight a common enemy. Maybe Harry Potter and Naruto could join forces to defeat a powerful dark wizard or a rogue ninja.
Well, it could be that God appears to Harry in a moment of great despair. He might show Harry the true nature of life and death in the wizarding world. Harry could learn about the deeper meaning behind the magic he wields and how it is all part of a greater plan designed by God. God could also guide Harry on how to use his powers more morally and justly, not just for the sake of defeating the Dark Lord but also for the betterment of the entire wizarding community.
Well, perhaps Harry Potter could use his magic against Shendu's dark powers. For example, he might try to counter Shendu's spells with his own powerful incantations like Expelliarmus. It would be an epic battle of magic from two different fictional universes.
One possibility is that Medusa is somehow brought into the Hogwarts grounds. This would cause chaos among the students and teachers. Harry, being the hero he is, would step up. He might research ancient spells and potions to deal with Medusa. He could also enlist the help of his friends like Hermione, who would dig into the library to find any information about Medusa in the wizarding world's history, and Ron, who would be there for moral support and also to help in any practical ways they could come up with.
One possibility is that Harry would learn the real motives behind some of the actions of the Hogwarts teachers. Maybe Dumbledore had some other reasons for keeping certain secrets from him all along. It could also be that the truth about the relationship between different magical creatures and wizards is revealed, like why some were always seen as more dangerous than they really were.
Well, it could be that the Cullens and Harry Potter team up against a common enemy. For example, a dark wizard who has some sort of connection to vampires. Harry could learn about the Cullens' way of life and they could learn about the wizarding world. There might be a cultural exchange of sorts, with Harry showing them things like butterbeer and the Cullens introducing him to their vampire traditions, if they have any.
Well, it could be really interesting. Maybe Anubis takes Harry on a journey through the Egyptian underworld in the fanfiction. Harry, being used to the wizarding world of Hogwarts, would be exposed to a whole new set of rules and magic in this strange underworld. He could meet other Egyptian deities and gain knowledge that would be useful in his own magical battles back in the UK.
There could be a situation where Nagini is in a weakened state for some reason. Harry, being the hero he is, might face an internal struggle. On one hand, he knows Nagini is Voldemort's pet and has been involved in many evil deeds. But on the other hand, he might see her as a victim of Voldemort's dark magic. So he could either try to kill her or try to free her from Voldemort's control.
In this fanfiction, Harry could learn ancient magic directly from the founders. Maybe he'd get special training from Godric Gryffindor in courage - based spells, or study potion - making secrets from Helga Hufflepuff.