Perhaps the magic in the Harry Potter world starts to seep into the DC Universe due to a dimensional rift. Harry teams up with the Justice League to close the rift before chaos ensues. He could teach some of the members basic magic spells for self - defense against the magical creatures coming through.
One idea could be that Harry Potter is magically transported to the DC Universe and is mistaken for a meta - human. The Justice League initially views him with suspicion but then realizes his unique magical abilities could be an asset in fighting a new, magic - based threat.
Perhaps in the fanfiction, Voldemort teams up with some of the Justice League's villains. This would force the heroes from both universes to work together. The wizards could teach the superheroes about magical defenses, and the superheroes could share their combat and strategic skills. Also, imagine Hermione tutoring Batman on advanced magical theories. It would be really cool to see how their different worlds' knowledge would interact.
One idea could be a crossover where the Young Justice team has to team up with the Justice League to face an interdimensional threat. Maybe a powerful villain from another dimension is trying to invade Earth and the combined skills and powers of both groups are needed to stop it.
Maybe a story where some of the younger members of the Young Justice team are frustrated with the Justice League's methods and decide to take on a mission on their own, but end up getting in over their heads and have to call in the League for help. This could lead to a lot of character development and some interesting dynamics between the two groups.
In a 'Harry Potter Harem Justice League Fanfiction', it could start with Harry being transported to the Justice League's universe. He discovers that his magic is a unique power there. The harem might form as the female members of the League, like Hawkgirl and Black Canary, are intrigued by this new 'wizard' in their midst. Meanwhile, they all figure out that an old enemy of the League has teamed up with Death Eaters from Harry's world. So, they train Harry in their ways and he teaches them some magic, all while dealing with the budding relationships.
One idea could be that the Justice League members gain new gaming - related powers. For example, Superman could have the ability to instantly analyze any opponent's weaknesses like a game character stats screen. Batman could use his detective skills to hack into virtual reality systems within the story's universe.
One idea could be a story where Batman has to lead the Justice League in a fight against a new, powerful and mysterious villain that can manipulate time. Another could be a fanfiction exploring the relationships within the Justice League when they are stranded on an uninhabited planet and have to rely on each other more than ever.
Perhaps in the fanfiction, there is a parallel universe where the Justice League are all vampires. They are trying to protect both the vampire and human populations from a greater evil that threatens to destroy both. They face challenges in getting the human - dominated Justice League in our universe to trust them and work together.
Maybe in the fanfiction, a new gamer is suddenly given the power to control the Justice League in a game, but they soon realize that their actions in the game are having real - world consequences, and they must team up with the heroes to set things right. This could lead to some really interesting character interactions as the inexperienced gamer tries to communicate with the heroes.
A crossover with the Avengers. Picture the Justice League and the Avengers having to work together to stop an interdimensional threat. There would be clashes in leadership styles between Captain America and Superman, and also a lot of cool moments as different power - sets are combined to fight the enemy.
One idea could be X23 joining the Justice League on a mission to stop a powerful mutant - hating villain. Her unique combat skills and mutant abilities would add an interesting dynamic to the team.