Poor Clary has it rough in this installment of the Mortal Instruments. Her mom's in a coma, her best friend's in love with her (the feeling isn't mutual), and she wants to get it on Marvin Gaye-style with her own brother. Sheesh. Kids these days, with their loud music and their Instagrams and their incest.
On the plot side of things, Clary doesn't quite fit in there either. She always wants to help Jace and pals fight Valentine's demons, but she's terrible at it, always getting knocked over, carried away, or otherwise incapacitated without helping out in the fight at all. She can't even shut a car door on her own, as we see in one scene where "Jace reached across Clary and jerked [the door] shut" (3.16.151).
Angelina Jolie or Scarlett Johansson she ain't. If you removed Clary from this book, very little would actually change. Heck, the good guys might actually do better with her out of the way.
Clary's major contribution is her wondrous ability to make new Runes. The Faerie Queen says that Clary has "the gift of words that cannot be spoken" (2.8.362). And she's not talking about a skill in speaking Latin, either. Clary discovers that she can create new protective Runes, and she uses it to draw a Fearless rune, one that makes people, well, Fearless. That sure comes in handy when the main nemesis in the book isn't just a demon of fear but the demon of fear.
When she's not getting trampled by demons, she's kinda sorta leading on her best friend, Simon. Simon has recently developed the courage to show his romantic feelings toward Clary, but she doesn't have the courage to tell him she's not interested. She only has eyes for Jace, who happens to be her brother.
After kissing Jace in the Seelie Court, Clary realizes how much she's hurting Simon. She's not just hurting him, either, she's killing him. Simon, hurt by Clary's feelings for Jace, basically kills himself when he goes to the vampire nest and becomes a vampire. Of course, Clary makes it all about herself, turning herself into some sort of martyr:
She'd never touch [Jace] again. That was her penance, her payment for what she'd done to Simon. (2.11.58)
Simon has to die not once, but twice before Clary realizes that they're not meant to be. Actually, that's giving Clary too much credit. It's Simon who calls it quits with her.
At the end of the book, after using her super runes to destroy Valentine's ship, Clary decides that she wants to be with Jace, incest taboo be damned. Unfortunately, he's decided that he doesn't want to be with her, and instead of speaking up for herself, once again she lets him make all the decisions for them:
I'll just be your brother from now on […] That's what you wanted, isn't it? (Epilogue.151)
It isn't, but she says it is. When will she realize that keeping her mouth shut isn't doing her any good? Speak up, Clary!