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.
There's a fanfiction called 'Jonathan's Redemption Arc with Clary'. It starts with Jonathan realizing the error of his ways and trying to make amends with Clary. The story goes deep into his internal struggle and how Clary responds to his attempts at change. Another one is 'Clary and Jonathan: Beyond Enmity' which imagines a scenario where they have to team up to save the Shadowhunter world from a greater threat, and in the process, their relationship evolves in a very different direction.
One popular one might be 'The Unseen Bond'. It delves deep into their relationship, showing how they support each other through various challenges in the Shadowhunter world. Their interactions are beautifully written, with a lot of emotional depth.
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.
One possible plot could be Clary using her shadowhunter skills to try and escape from Jonathan's clutches. Maybe she finds a hidden weapon or a secret passage in the place where she's held captive.
Well, perhaps there's a plot where they discover some ancient prophecy related to their baby during the pregnancy. And they spend the whole time trying to figure out what it means and how to ensure their child's safety according to the prophecy. They might seek help from different factions in their world, like the Shadowhunters or Downworlders.
A possible direction for the fanfiction is that it delves into the backstories of Clary and Jonathan in relation to the pregnancy. Perhaps there are family secrets or prophecies that are now coming to light because of the baby. It could be that there are certain powers or abilities that the child is expected to inherit, which adds another layer of complexity. The story could also show how they interact with other characters during this time. Some characters might offer help and support, while others might try to take advantage of the situation for their own gain.
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.
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.
Clary's family has always been protective of her. So, they would likely be very cautious about this pregnancy. Her father figure, if he's still around, might want to ensure that Jonathan is worthy of being in Clary's and the baby's life. They might put Jonathan through a series of tests or challenges to prove his commitment. On Jonathan's family side, if they are part of a more villainous group, they could see the baby as a tool for their own evil plans. Or, if there are some good - hearted members, they might try to guide Jonathan and Clary towards a more positive future together.
You can try Archive of Our Own (AO3). It has a large collection of fanfiction, including those about Jonathan and Clary. Just use the search function and type in their names.
One great Clary and Percy fanfiction is 'The Unlikely Alliance'. It combines their unique personalities in an exciting adventure. Another one could be 'Clary and Percy: A New World' which explores how they would interact in a different magical realm. There's also 'Clary's Encounter with Percy' that delves into their first meeting and the initial spark of their relationship.