One idea could be that Harry discovers he has a strange connection to the Pokémon world. As an Animagus, he could transform into a form that has some similarities to Mewtwo, like having purple eyes or telepathic abilities. Maybe he gets transported to a world where Pokémon exist and has to use his skills as an Animagus and wizard to survive.
Imagine a story where Harry, in his Animagus form, is mistaken for a new and mysterious Pokémon by some Pokémon trainers. Mewtwo, being intrigued by this strange being that seems to have both Pokémon - like abilities and human intelligence, decides to help Harry. Together, they explore the differences and similarities between the two worlds, learning from each other's powers and cultures.
It could start with Harry having a strange dream about a powerful purple - colored creature. When he wakes up, he starts to notice some odd changes in his Animagus abilities. He might find that he can sense things in a way that's not normal for a wizard or a regular Animagus. Then, one day, he suddenly gets pulled into a portal and finds himself in a world full of Pokémon, where he meets Mewtwo right away.
Perhaps a story about an adult wizard who was cursed and turned into a unicorn animagus against his will. He then has to navigate the wizarding world in this new form, facing prejudice from some who don't understand his condition. Along the way, he meets Harry Potter and his friends, who help him find a way to break the curse.
One idea could be that Harry discovers he is a Hydra Animagus in a very dangerous situation. Maybe when he is facing Voldemort and his Death Eaters, he suddenly transforms into a Hydra, taking them by surprise. The multiple heads of the Hydra could have different abilities, like one head spits fire, another can freeze things, and it gives him an edge in the battle.
In a fanfiction, Harry as a Quetzalcoatl Animagus could play a crucial role in a battle against Voldemort. His Animagus form could be resistant to certain dark spells, and he could use the large size and strength of the Quetzalcoatl to his advantage. Maybe he could also communicate with magical creatures from the Americas that are drawn to his new form, and they could help in the fight against the Death Eaters.
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.
One idea could be an animagus who uses martial arts skills in the wizarding world. For example, an animagus who turns into a panther and combines its natural agility with martial arts moves to fight dark wizards. They could have learned martial arts in the Muggle world and then incorporated it into their magical abilities when they discovered they were an animagus.
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.
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.
Well, an idea could be that a group of Hogwarts students discover a hidden portal that leads to the Pokemon world. There, they learn about the Pokemon's unique abilities which are somewhat similar to magic in their world. One of the students realizes they can transform into a Pokemon in the same way as an Animagus. They then bring this knowledge back to Hogwarts and start a new study group on it.