One interesting plot idea could be Naruto's chakra system interacting with magic in the Harry Potter world. For example, his ability to use shadow clones might be seen as a form of magic by the wizards. Another idea could be Naruto being sorted into a Hogwarts house, perhaps Gryffindor because of his courage. Or maybe he could teach the Hogwarts students some of his ninja skills in a special class.
One interesting plot idea could be that Fem Naruto, with her ninja skills, enters the Twilight world. She might get involved in the vampire - werewolf conflict. For example, her ability to sense danger could be a great asset. Another idea is a love triangle between Fem Naruto, Edward, and Jacob. Her strong - willed nature would add a new dynamic to the relationship.
Imagine if the Marauder's Map could show the layout of Narnia. Harry and his friends could use it to navigate through Narnia, which would be a huge advantage. But then, there could be a twist where the map starts to malfunction in Narnia because the magic there is different. And a character like Mr. Tumnus could be revealed to have some connection to the wizarding world in Harry Potter. Maybe he was once a wizard who was exiled to Narnia and lost his magic, but regains it when the two worlds start to interact.
One interesting plot twist could be that the Death Eaters in the Harry Potter world form an alliance with the Britannian Empire from Code Geass. This would create a powerful and evil force that the protagonists from both worlds would have to fight against. Another could be that a character like Lelouch, with his Geass power, gets transported to Hogwarts and uses his wits and power to outmaneuver Voldemort. Maybe he could even use his Geass on some of Voldemort's followers to turn them against him.
One interesting plot idea could be a battle between the hunters from Supernatural and the vampires from Vampire Diaries. Maybe the Winchesters end up in Mystic Falls and think all the vampires there need to be hunted. Another idea is a character swap. For example, Castiel could end up in the Vampire Diaries world and interact with the characters there in a very different way compared to his usual interactions in Supernatural. A third idea could be a joint mission to fight a greater evil that threatens both universes, like an ancient demon that wants to use the power of the vampires in Vampire Diaries and the magic from Supernatural for its own dark purposes.
Perhaps a plot where the Persona characters are invited to a special tournament in the Senran Kagura world. The tournament has strange rules that are different from what they are used to. As they participate, they start to notice some dark undercurrents. It turns out that an enemy is using the tournament to drain the energy of the combatants for a nefarious plan. The Senran Kagura and Persona characters must then put aside their differences and work together. The Persona characters can use their Personas to analyze the situation and the Senran Kagura characters can use their combat expertise to fight the physical battles.
One interesting plot idea could be the combination of the technology from Mass Effect and the world - building of Anthem. For example, Shepard could find himself in the world of Anthem and have to adapt to the javelin exosuits while also dealing with the local threats. Maybe the Reapers start to target the world of Anthem as well, and the two groups from different universes have to team up to fight this common enemy.
Perhaps a plot where Naruto is influenced by an evil godlike entity. This entity could be from a different dimension. It whispers dark thoughts into Naruto's mind, gradually turning him against the values he once held dear. As a result, he starts to perform actions that are completely out of character for the original Naruto, like attacking innocent villages to gain more power.
Maybe some of the Hogwarts students are sent to the Naruto universe. They would be amazed by the ninja techniques. Hermione, for instance, would be eager to study how chakra works and might even find a way to combine it with magic. Harry could learn some ninja stealth skills which would be useful in his fight against Voldemort.
One popular idea is a battle royale - where the powerful characters from Naruto and Fairy Tail compete. Another is a team - up against a common, super - powerful enemy. For example, Naruto's Rasengan combined with Natsu's Fire Dragon's Roar could be a really cool and powerful attack.
A common exciting plot point is when Naruto characters use their unique abilities in the wizarding world. For example, when Naruto uses his shadow clone jutsu to outwit magical creatures or solve problems that the wizards can't. It creates a sense of novelty and power.