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.
One plot could be that Clary's memories are locked away in a magical realm. She has to go on a dangerous quest to this realm to retrieve them. Along the way, she meets different creatures and overcomes various obstacles. Another interesting idea is that her memories are scattered among different people. So she has to travel around and meet these people, and each encounter gives her back a part of her memory. Also, it could be that her memories are being held hostage by a dark force, and she has to battle this force to get them back.
In some fanfictions, Clary might get her memories back in a dream. She dreams of her past life and relationships, and when she wakes up, she starts to remember bits and pieces. Or perhaps there's a new character introduced who has the power to restore memories, but at a cost. Clary has to make a difficult decision to fully regain her memories. Another plot could be that Clary's memories are tied to a prophecy, and as she gets them back, she discovers her true role in a much larger scheme.