It could also be that he is influenced by the people around him. His friends or family in the fanfiction might encourage him to open his heart again. And this new relationship gives him a different perspective on love. The woman (or man) he decides to marry might have a unique charm that makes him believe in a new future together.
One reason could be that he has finally healed from his past traumas. Maybe he has found someone who truly understands his complex life as a former military man and friend of Sherlock. This new person might bring a sense of stability and normalcy that he has been longing for.
Another possibility is that he marries someone related to Sherlock's world. Maybe a detective or an investigator who he meets during one of Sherlock's cases. They start off as colleagues in solving the mystery and gradually develop feelings for each other.
One possible reason could be that Adrien is being blackmailed by Hawkmoth. Maybe Hawkmoth has some information or has threatened someone Adrien cares about deeply, like his friends or family. So, in order to protect them, he decides to help Hawkmoth, even though he knows it's wrong.
One possible reason could be for a mission. Maybe in the fanfiction, there is a mission that requires Naruto to go undercover as a girl. This would allow him to access certain places or information that would be otherwise unavailable to him as a boy. Another reason might be for self - discovery. Naruto could be curious about what it's like to be a girl and decides to explore that side of himself in the fictional world.
John could get injured due to the actions of a villain. The villain might set a trap for him. For instance, the villain could rig a staircase to collapse when John steps on it. This would cause John to fall and get injured, perhaps with broken bones or internal bleeding, as part of the villain's evil plan to stop John from achieving his goals.
One common theme is the struggle with identity. As a vampire, John has to reconcile his new vampiric self with his old identity as a doctor and a friend. Another theme is the relationship with Sherlock. It often becomes more intense and complicated due to his vampiric nature.
One common theme is the exploration of gender roles. Since John is female in these fictions, it often looks at how she navigates a world that was originally male - dominated in the Sherlock Holmes canon. Another theme is relationships, like her friendship with Sherlock or potential romantic relationships. Also, the theme of her proving herself in a male - dominated field, such as detective work, is quite prevalent.
One common theme is friendship. Writers often explore how an original character can form a deep and meaningful friendship with Watson. It could be a friendship that helps Watson through tough times or one that adds a new dimension to his life.
Often, there's a theme of using his skills. His medical knowledge and deductive reasoning are put to use in the Avengers' context. Also, there can be a theme of culture clash. John Watson comes from a different sort of world in the Sherlock Holmes stories, and his values and ways of doing things might clash or blend with the Avengers' way of life.
Another issue might be that it can be off - putting to many fans. Most fans love the original relationships and personalities in the source material. Abusive fanfiction can create a negative view and might not be in line with the positive community that usually surrounds a fandom.
Yes, there are quite a few. You can start by looking on fanfiction websites like Archive of Our Own. There are stories that might bring John Watson into the Avengers universe in really interesting ways, like making him a consultant for the team due to his medical and detective skills.