There are quite a few potential plotlines. For example, imagine that a powerful magical artifact from the Harry Potter universe is stolen by Loki and he uses it to create chaos in both the Avengers' world and the wizarding world. At the same time, a character with the same unpredictable nature as Ledger's Joker emerges in the mix. The Avengers and Harry Potter characters would have to put aside their differences and use their unique abilities. The wizards could use their magic, the Avengers their superpowers, and they'd all have to deal with Loki's trickery and the chaos - causing character, leading to a complex and exciting adventure.
A possible plotline might start with Loki being banished from Asgard again, but this time he lands in the world of Harry Potter. He begins to learn about magic and decides to use it for his own gain. Meanwhile, in the Avengers world, a new villain inspired by Ledger's Joker is causing trouble. The Avengers try to stop this villain while also realizing that Loki's actions in the Harry Potter world are somehow connected. Eventually, the Avengers find a way to enter the Harry Potter world, and with the help of the Hogwarts students and teachers, they face off against Loki and the Joker - like villain, with a lot of action, magic, and superpower - based battles along the way.
I'm not sure there are many that combine all of these specifically. However, there might be some out there that cross Avengers and Harry Potter universes, but adding Ledger (presumably Heath Ledger's Joker) and Loki in the same fanfic would be quite rare. You could try searching on big fanfiction websites like Archive of Our Own.
One possible plotline could be a struggle for power. Since Loki is often associated with power - seeking in Norse mythology and Harry has her own power in the wizarding world, they might fight or cooperate in a bid for more power across both realms. Another could be a story of acceptance, where they have to deal with the shock and disbelief of their respective friends and families. For example, the Weasleys might be horrified at Harry's new 'marriage' and the Norse gods might be equally shocked.
A possible plotline could be that Harry, after the war, is magically bound to Narcissa for some reason. In the harem setting, other characters like Luna or Ginny could also be part of it. Harry has to figure out how to balance his relationships while also dealing with the post - war wizarding world. Narcissa might use her influence to protect Harry from those who still hold grudges against him.
A possible plotline is that Harry grows up in a world where magic and technology co - exist. He uses his combined heritage to solve mysteries that neither wizards nor superheroes could alone. For instance, he might use his knowledge of magic to fix a malfunctioning Stark tech device that has been enchanted. Or he could use Stark - made gadgets to enhance his magic in battles against dark wizards. His relationships with characters like Hermione and Thor would also be central to the story, as they help him understand his two sides.
One possible plotline could be that Harry's half - sister is initially on the side of the dark forces. She could be manipulated by Voldemort or his followers. Harry then has to try and save her and turn her to the good side. This would be a classic good - vs - evil struggle within the family.
It could be that a powerful sorcerer in the Avengers' world goes rogue and starts using dark magic. The Avengers don't know how to handle magic, so Harry is called in. He has to face this rogue sorcerer, using his own brand of light magic. Along the way, he might have some clashes with the Avengers' way of doing things, but in the end, they all work together and Harry manages to save the day by defeating the rogue sorcerer and restoring peace in the Avengers' world.
One idea could be a crossover where Fenrir from the Harry Potter universe somehow gets transported to the realm of Loki. Loki, being the trickster, might see Fenrir as a tool for his own schemes. Harry Potter, perhaps in a quest to stop some dark magic related to Fenrir, ends up following him and has to deal with Loki's antics as well.
Perhaps the lemon is a key element in a prophecy. In this fanfiction, Catelyn has a vision that involves a lemon, Arya, and elements from the Harry Potter universe such as Hogwarts. Arya is on a quest to find out more about this prophecy. She teams up with characters from both worlds, and together they try to decipher the meaning of the lemon in the prophecy. It could be that the lemon represents a source of power that can either save or destroy their world, much like the Horcruxes in Harry Potter.
One possible plotline could be that in a magical crossover world, Harry Potter somehow stumbles into the world of Leah Clearwater. Maybe the lemon aspect could be a magical fruit with special powers that they have to find together. They could face various challenges along the way, like dark wizards who also want the lemon for its power.
One possible plotline could be a blind character in the 'Harry Potter' world who has a special ability related to their blindness. Maybe they can'see' magic in a different way than others, like being able to sense dark magic more acutely. In a 'Lord of the Rings' context, a blind character might have an enhanced sense of hearing or smell to compensate, and they could play a crucial role in the quest, like being able to detect approaching enemies from afar.