One possible plot could be that Harry Potter is somehow transported to the world of Samurai Jack. He teams up with Jack to fight Aku. Harry uses his magic, like the Patronus charm to fend off Aku's dark minions, while Jack uses his sword skills. Their combined powers and different fighting styles make them a formidable duo against Aku's tyranny.
Well, perhaps in this fanfiction, Laughing Jack somehow finds his way into Hogwarts. He starts causing chaos in the school, like making the staircases move erratically or turning the portraits into creepy, distorted versions of themselves. Harry Potter then has to figure out a way to stop Laughing Jack without using dark magic. He might seek help from Dumbledore and use his knowledge of both the wizarding world and his own courage to face this new threat.
Well, it could be that Jack Frost accidentally ends up in the wizarding world. Maybe he freezes some of the Hogwarts grounds and Harry and his friends have to figure out how to unfreeze it without magic harming Jack.
It could be Aku. Since he is the main villain in Samurai Jack's world, his power and evil nature would make him a great antagonist. He could see Harry's magic as a threat and try to eliminate him. And if he teams up with some of the dark forces from the Harry Potter universe like Voldemort or the Death Eaters, it would be even more challenging for Harry and Jack.
Perhaps the plot could start with Naruto finding an old, tattered scroll that shows the adventures of Samurai Jack. Naruto becomes obsessed with Jack's story and starts to train in a way that combines his ninja training with what he thinks Samurai Jack would do. As he progresses, he starts to have visions of Jack's world. Eventually, he finds a way to cross over. In Jack's world, Naruto uses his ninjutsu in creative ways to help Jack in his fight against Aku. In return, Jack teaches Naruto the art of the samurai, and Naruto brings these new skills back to his own world to face his enemies in a different way.
Maybe in the fanfiction, Harry accidentally enters a parallel dimension where Lily is still alive. Here, Lily discovers that Harry is her future son. She might take him under her wing and train him in a different way of magic, one that was perhaps forgotten in Harry's own time. This could lead to Harry having unique powers and a different approach to dealing with the Dark Arts and his enemies.
A plot could involve Sherlock being a wizard all along but not realizing it until he meets Harry Potter. He has been using his logical mind to do what he thought was normal detective work, but it was actually his latent magic powers at play. Together, they could solve crimes in both the Muggle and wizarding worlds, using Sherlock's methods and Harry's knowledge of magic spells and potions.
One possible plot could be that the magical creatures in the Harry Potter world start to show up in Forks. For example, a hippogriff might fly over the forest near Bella's house, causing chaos among the vampires and werewolves. The wizards from Hogwarts could come to investigate these strange new creatures that seem to have a different kind of magic than what they're used to. Harry, Hermione, and Ron could find themselves in the middle of the vampire - werewolf feud, trying to figure out how to keep the peace and also protect the muggles in Forks from getting too involved in this new magical mess.
In this fanfiction, a new teacher arrives at Hogwarts who has a passion for both magic and glee. This teacher decides to start a glee - like club at Hogwarts. Harry and his friends are intrigued and join. They discover that music has a special power in the wizarding world. It can be used to unlock hidden magical abilities. The club then prepares for a big magical glee competition against other magical schools, with each performance having a unique magical twist.
Well, perhaps Byako is a being from another dimension. In the 'Harry Potter meets Byako fanfiction', Byako could accidentally cross over into the Harry Potter universe while being chased by some sort of other - dimensional foe. Harry and his friends could help Byako hide from this enemy while also learning about different forms of magic from Byako's world.
Perhaps in the fanfiction, the Ministry of Magic mistakes Loki for a powerful dark wizard. They try to capture him, but Loki easily evades their attempts. Harry Potter, being curious, decides to find out who this strange wizard is on his own. When they meet, Loki is initially hostile, but as they start to talk, they realize they both have a lot in common in terms of fighting against powerful and often misunderstood forces. They then form an uneasy alliance to face a new threat that is emerging in both their worlds.