One key element is the exploration of their relationship. Since they have a very different relationship compared to the canon where Jonathan is more of an antagonist, in these fanfics, their bond as siblings or comrades growing up together is a major focus.
There's also 'Clary and Jonathan: Sibling Ties'. This fanfic delves deep into how their upbringing together affects their personalities. It shows Clary's struggle to understand Jonathan's darker side while still feeling a sense of loyalty due to their shared upbringing. It's a really interesting read as it reimagines their relationship dynamics.
Alec and Isabelle could be important characters too. As part of the shadowhunter group, they have the skills and resources to track down Jonathan. They could be the ones who gather intelligence on Jonathan's whereabouts and plan the rescue strategy, while also dealing with their own personal issues and relationships within the group.
Fanfiction might be a way for Jonathan and Clary to express their own creativity vicariously. Even if they are not writing it themselves, by reading and loving different fanfiction stories, they are engaging with the creativity of other fans. It's like they are part of a larger creative process. Additionally, it could be a form of emotional investment. They might be so attached to the characters in the original story that they want to see more of their lives and adventures, and fanfiction provides that in abundance.
Well, 'Clary and Jonathan: The Hidden Path' is quite interesting. In this fanfiction, it takes the idea of a prophecy that ties their fates in a way not seen in the original story. It's full of mystery and unexpected twists. Also, 'The Shared Destiny' is a fanfic that focuses on their powers and how they could be combined in unique ways if they were to work together instead of being at odds all the time.
In this fanfiction, the two main characters are Jonathan and Clary. Jonathan's character might be developed further as he adjusts to the idea of being a father. He may have to make sacrifices and grow in ways he hadn't expected. Clary, as the pregnant one, is likely to be the focus of much of the story's emotional core. She'll be dealing with hormonal changes, fears about motherhood, and the added pressure of having a baby in a world filled with danger and magic.
One great Jonathan x Clary fanfiction is 'The Unlikely Bond'. It explores their complex relationship in a unique way, delving into their shared history and how it could have led to different outcomes. Another is 'A Different Path' which imagines a world where they work together against common enemies and in the process, form a deep connection. And 'The Hidden Feelings' is also interesting as it uncovers the repressed emotions between them.
You can start by looking on Archive of Our Own (AO3). It has a vast collection of fanfictions, and there are likely many Jonathan x Clary ones there. Fanfiction.net is also a good place to search. There are numerous stories on different fandoms, and you should be able to find some related to Jonathan and Clary.
One interesting aspect could be the creativity it shows. Fanfiction allows them to explore different scenarios and relationships for their favorite characters that might not be in the original story. It gives them a chance to delve deeper into the fictional world they love.
People like to write Clary and Jonathan fanfiction because their relationship in the original story is so complex. There's a lot of room to explore different 'what - ifs'. For example, what if Jonathan wasn't completely evil? Writers can play with their characters' personalities and create new storylines.