Jace would likely be an important character. Given his relationship with Clary, he would probably be deeply affected by the news of the baby. His reaction could range from shock to protectiveness.
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.
Jace could be the father. Since they have a strong connection in the original story, it would make sense for him to be the father in the fanfiction.
Maybe in the fanfiction, the father of the baby is a mystery. Clary has to deal with the speculation and rumors around who the father could be while also taking care of her little one. It could add a lot of drama to the story as she might face accusations or unwanted attention.
Alec might also come to her rescue. As a skilled Shadowhunter, he has a strong sense of duty. Plus, he's part of Clary's group, and he wouldn't stand by and let a fellow Shadowhunter be attacked by a demon.
The main characters are Clary and Jace. Clary is a strong - willed character, often in the middle of adventures in the Shadowhunter world. Jace is a skilled Shadowhunter, and together they form a central couple in this fanfiction, especially with the new situation of Clary being pregnant.
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.
In this fanfiction, Clary is likely a newly introduced and attractive female character. However, without more context from the specific fanfiction, it's hard to say more about her personality or role in the story.
Another character who has a personal vendetta against Clary or her family. For example, a jealous rival or someone who blames her family for past misfortunes. This would add a layer of drama and personal conflict to the fanfiction.
One possible plot could be Clary adjusting to motherhood while still dealing with her shadowhunter duties. Maybe she has to protect the baby from demons who are after it because of its special powers.
Obviously, Clary herself is the most important character as she's the one giving birth. Her partner would also be crucial, providing support and sharing the joy of the new arrival.