Well, one interesting plot could be Clary slowly regaining her memories through a series of magical encounters. Maybe she finds an old object that triggers flashes of her past. Another could be that her friends play a crucial role in helping her get her memories back, like they take her to special places related to her past. And a third possibility is that there's some sort of enemy who is trying to stop her from getting her memories back, which adds a lot of suspense to the story.
Clary is the central figure. Valentine might also be involved in some fanfictions, either as an obstacle trying to prevent Clary from getting her memories back because he doesn't want her to discover certain secrets, or in a more complex way where his past actions are somehow related to the loss of her memories in the first place. And of course, the Lightwood family members are likely to be involved, given their importance in Clary's life and the Shadowhunter community.
With her friends, like Alec and Isabelle, it might change the dynamics a bit. They might be more cautious about training with her in the future. Or they could see her as more vulnerable and start to include her in different, less dangerous activities within the Shadowhunter world.
Simon might be in a bit of a panic. Since he's her friend and also not as used to the dangerous situations as the other Shadowhunters. He'd try to do whatever he can to help, like getting help from more experienced Shadowhunters or trying to comfort Clary while she's in pain.
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 theme of future and responsibility is also often explored. Clary has to think about not only her own future but also the future of the baby. This includes things like where she'll live, how she'll raise the child, and how it will impact her goals and dreams. For example, if she was in the middle of some important mission or study, the pregnancy will force her to reevaluate all those aspects of her life.
Well, she might be rescued by her friends. In many fanfictions, her Shadowhunter comrades would come to her aid, using their unique skills to fend off the attackers.
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.
On the other hand, there could be a glimmer of hope in their relationship. Maybe through the shared experience of the pregnancy, they start to see the good in each other. Clary might see a side of Sebastian that she never knew existed, and Sebastian might start to have real feelings for Clary and the baby, leading to a more complex and evolving relationship.