One plotline could be that the 'Spider King' has some sort of ancient grudge against the wizarding world in 'Harry Potter'. His minions start to infiltrate Hogwarts, and the students have to use their magic to fight back. Another could be that a prophecy in the 'Harry Potter' world mentions the 'Spider King', and Harry is tasked with finding out more about this new threat.
One plotline could be Moriarty infiltrating Hogwarts as a new teacher. He could secretly be plotting to steal powerful magical artifacts while also manipulating the students and staff. Harry and his friends would start to notice strange things happening around the school and suspect the new teacher. Another could be that Moriarty teams up with Voldemort, combining their evil minds to take over both the wizarding world and the Muggle world. This would put Harry in an even more difficult situation as he has to face two powerful villains at once.
One potential plotline could be that Harry discovers he has a bijuu sealed within him. This could explain some of his strange powers or abilities that are not accounted for in the original series. As he grows older, he has to learn to control this bijuu power, while also dealing with the usual threats in the wizarding world like Voldemort.
One possible plotline could be Shirou finding himself magically transported to the Harry Potter world. He might use his skills in magic and combat from his own world to help Harry and his friends in their battles against Voldemort. For example, Shirou's ability to project weapons could be a unique advantage in the wizarding world.
One potential plotline is that a powerful artifact in the Harry Potter world has the ability to grant the wielder access to other dimensions, and it accidentally pulls Cloud into the wizarding world. Cloud, not understanding the ways of this new world at first, is seen as a threat. Harry and his friends have to decide whether to trust him or not. As they get to know Cloud, they realize his skills can be useful in their fight against the Death Eaters.
Maybe the baby dragon is a rare species. This would attract the attention of magical zoologists and collectors. Harry would then have to deal with the ethical issues of keeping the dragon or giving it to those who claim to study it properly. He would also need to consider the dragon's own well - being and freedom.
One plotline could be that a group of rogue wizards discovers how to create a nuclear - like magical weapon, similar to a nuclear bomb. They plan to use it to take over the wizarding world. Another could be that the Muggle world's nuclear technology somehow leaks into the wizarding world and causes chaos as wizards don't understand it at first. Or maybe Voldemort gets hold of a nuclear bomb through some Muggle - loving Death Eaters and tries to use it against both the Muggle and wizarding worlds.
One plotline could be a time - travel scenario. Harry goes back in time and somehow ends up changing Lucius' path before he becomes a full - blown Death Eater. This alteration in Lucius' life leads to a different relationship developing between them, which could end in marriage. Another could be a situation where they are both under the influence of a powerful magic that makes them see each other in a new light, and they fall in love despite their differences.
One plotline could be Sherlock growing up with some sort of magical ability that he has to hide in the Muggle world. Since Harry Potter is his father, he might inherit some latent magic. He could use this in his detective work, like being able to sense when someone is lying in a way that's more than just normal intuition, because of his magical heritage.
Well, there could be a plot where Harry, in his quest to defeat Voldemort once and for all, stumbles upon blood magic as a last resort. He might initially be hesitant but as the situation becomes more dire, he starts to explore its depths. Or perhaps, he is influenced by a new character who claims to be an expert in a different form of magic that includes blood magic, and Harry is drawn into it, believing it could give him an edge in the ongoing battle against the dark forces.
For the Atlantis side, there could be Atlantean royalty, like a princess or a group of elders. There might also be Atlantean mages or warriors. And don't forget about the mer - people. They could play a role, either as allies or antagonists. Maybe there's a mermaid who falls in love with Harry and helps him understand the ways of Atlantis.