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.
She might have to take a break from training. This could set her progress back. Maybe she'll feel frustrated and more determined to get better once she recovers.
Obviously, Wolverine himself is the central character. But other X - Men members could be involved. Professor X might play a role as he could help Wolverine make sense of his newly recovered memories. He could use his telepathy to guide Wolverine through the maze of his past.
One interesting scenario could be Wolverine remembering his past relationships. He might suddenly recall an old love, like Jean Grey perhaps, and how they interacted before. This could lead to some complex emotional moments as he tries to reconcile his new self with the memories of his past feelings.
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.
Or, in a more creative take, it could be a new character introduced just for this fanfic. This new character could bring a whole new set of dynamics and storylines, like a mysterious stranger who has some special connection to Clary.