One idea could be that Harry Potter, as an Animagus, somehow gets transported to the Marvel universe. He could team up with the Avengers in his animal form, perhaps using his unique abilities to gather intelligence. For example, as a stag, he could move quickly and unnoticed in certain terrains, providing valuable information to the Avengers before a battle.
Maybe an Avenger, like Natasha Romanoff, discovers she has the potential to be an Animagus. She could learn from Harry Potter's knowledge. In a fanfiction, they could be in a situation where they need to infiltrate a heavily guarded place. Harry teaches Natasha how to transform into an animal, and she uses her skills as a spy along with this new ability to complete the mission.
One idea could be a character in the Harry Potter universe who is secretly an Animagus but gets cursed and starts to show Wendigo - like traits. They struggle to control their newfound savage nature while also hiding it from their friends at Hogwarts.
A fanfic could involve a character from Twilight who discovers they have the potential to be a wolf animagus in the Harry Potter sense. They then have to travel to the wizarding world to learn how to control this new ability. This would bring in elements of both worlds, like the magic of Hogwarts and the vampire - werewolf - human dynamic of Twilight.
Perhaps a dark wizard uses magic to create an Animagus - Godzilla hybrid as a weapon. The Harry Potter gang has to find a way to stop this abomination. They might use their own Animagus forms to combat it. For example, Harry could turn into his stag Animagus and use its speed and agility to distract the Godzilla - Animagus while Hermione figures out a spell to reverse the dark magic.
Perhaps in a fanfiction, Voldemort has made an alliance with a powerful villain from the Avengers' world and an ancient order of Assassins gone bad. Harry Potter, along with some of his Hogwarts friends, has to convince the Avengers to help them. They would then combine their different abilities. For example, Hermione could use her vast knowledge to figure out the weaknesses of their enemies, while Captain America could lead the group in battle strategy, and the Assassin could provide crucial intel on the secret workings of the enemy alliance.
One idea could be a crossover where Hydra discovers the wizarding world in the Harry Potter universe and tries to use magic for their evil purposes. The Avengers somehow get wind of this and team up with Harry Potter and his friends to stop Hydra. Maybe they have to battle magical creatures that Hydra has corrupted with dark magic.
In a fanfiction, the Avengers could be called to the Harry Potter universe to help fight Voldemort. Black Widow would be a key player in infiltrating Death Eater strongholds. She could teach the Order of the Phoenix some of her combat and espionage techniques. And perhaps Harry Potter could gain some inspiration from the Avengers' teamwork and use it against Voldemort.
One idea could be a magical crossover where a spell goes wrong in the Harry Potter world and somehow links to the Avengers universe. A male character from either side could end up pregnant due to some strange magical - scientific mishap. For example, if Loki were to be affected by a Hogwarts spell that causes mpreg. It could lead to a lot of chaos as the Avengers try to figure out what happened while the Harry Potter characters deal with the consequences of their spell reaching another dimension.
One idea could be that the Deathly Hallows from Harry Potter have some sort of connection to the powers of the God of Death in the Avengers universe. Maybe the Elder Wand could be a weapon that has the power to control the souls like the Infinity Stones do in the Avengers. The Invisibility Cloak could be used by a character from the Avengers to sneak around in a world filled with magic, similar to how Harry used it at Hogwarts.
One idea could be that Selene finds herself magically transported to the wizarding world of Harry Potter. She might initially be confused but then use her skills as a vampire to help in some sort of battle against dark wizards. For example, her enhanced speed and strength could give the Order of the Phoenix an edge in a fight.
A fanfiction could involve Gabriel getting involved in the fight against Voldemort. He might use his trickster abilities to outwit Voldemort and his Death Eaters. For example, he could create illusions that confuse the enemy, which would give Harry and his allies an advantage in the battle.