A plot could involve Voldemort learning about the power of ADAM in Bioshock. He sees it as a way to gain ultimate power and sends his Death Eaters to Rapture to steal it. Meanwhile, a group of Aurors follow them, and then there's a three - way battle between the Aurors, Death Eaters, and the denizens of Rapture.
Well, it could be that a dark wizard in the Harry Potter universe discovers the ADAM and plasmids from Bioshock. He starts using them to create an army of super - powered Death Eaters. Harry and his allies have to figure out how to counter this new threat. They might travel to Rapture to find a way to neutralize the ADAM or find some kind of magical antidote. Harry could use his Patronus charm to fend off the more deranged splicers, and the Weasley twins could use their prank - making skills to mess with the Big Daddies.
Well, for a Harry Potter and Naruto crossover fanfic, a cool plot could be that there is a dark force emerging that is a combination of Voldemort's magic and the Akatsuki's evil intentions. Harry Potter and Naruto then join forces. They start by training together, with Naruto teaching Harry some basic ninja moves like tree - walking to improve his physical abilities, and Harry teaching Naruto some basic spells for protection. Along the way, they gather their friends from both worlds, Hermione and Sasuke for example, to fight against this new threat.
One idea could be a spell gone wrong in the wizarding world that somehow transports some Hogwarts students to Forks. They then have to deal with the vampire and werewolf situation there while also trying to find a way back home. Maybe Hermione could be intrigued by the science - like aspects of the Twilight world that seem so different from magic.
One idea could be that Quentin Coldwater from 'The Magicians' accidentally travels to the world of Harry Potter. He could be mistaken for a new exchange student at Hogwarts. He might try to use his Brakebills knowledge, like his unique spellcasting techniques, which would both amaze and confuse the Hogwarts students.
One idea could be that the Avengers are transported to the wizarding world. Iron Man could be fascinated by the magic technology and try to incorporate it into his suit. Another could be that Voldemort somehow gets hold of the Infinity Stones and the Avengers have to team up with Harry Potter and his friends to stop him. Maybe Thor's hammer could be enchanted by a Hogwarts spell to have new powers.
One idea could be that the characters from 'The Magicians' end up at Hogwarts for a magical exchange program. They'd have to adapt to the different magical rules and culture there. For example, Quentin might be fascinated by the concept of houses at Hogwarts, while Eliot could get into trouble for trying to introduce some of his more 'adult' magic tricks from Brakebills.
One idea could be that the Avatar characters gain the ability to use magic when they enter the Harry Potter world. For example, Aang could use his airbending skills along with magic spells to fight against the Death Eaters. Another could be that Hogwarts students are sent to the Avatar world for a special exchange program, and they have to learn to bend elements instead of casting spells.
One idea could be that Chuck, with his knowledge of the supernatural, ends up at Hogwarts. Maybe he's there to investigate some strange magical occurrences that are linked to his world's demons or angels. He could form an unlikely friendship with Harry Potter, and together they figure out how to stop a dark force that's using both magic and the powers from Chuck's universe.
One idea could be that Voldemort somehow makes an alliance with Loki. The Avengers would then have to team up with Harry, Hermione and Ron to stop them. They could combine magic and superpowers in battles. For example, Iron Man could use his technology to analyze and counter some of the dark magic spells while Harry uses his Patronus to protect the group from Loki's illusions.
One idea could be that Voldemort teams up with a powerful Marvel villain like Thanos. This would force the Avengers and the Harry Potter characters to join forces. The Avengers could bring their strength and high - tech weapons, while the Harry Potter characters use their magic. Another plot could be that a magical artifact from the Harry Potter world is lost in the Marvel universe and both groups have to search for it. Maybe it has the power to destroy both universes if misused.