Although Valentine has the Soul-Sword, the good guys need some kind of artifact too. After all, Harry Potter had the sorcerer's stone or his invisibility cloak. What do the Shadowhunters have?
Clary, who you may remember always enjoyed drawing, finds out that she can transform her idle doodles into real power by creating her own runes. Why? This isn't actually explained.
Most people take their amateur artistic abilities and try to make a few bucks on Etsy. Clary uses hers to fight evil. Based on a tip from the Faerie Queen, Clary decides to try her hand at creating a new rune. But what? A Rune of Beauty? Or Peace? Or infinite donuts? Nope, a Rune to eliminate fear:
"There are runes for bravery," said Jace. "But never anything to take away fear." (3.14.124)
Of course Clary does exactly what Jace wants, and whips up a Fearless Rune. They try it out on Alec and realize it works when he almost comes out as gay to his parents. In the climactic battle, Clary puts the Rune on Jace, which allows him to face down Agramon, the Fear Demon, with no fear.
The Fearless Rune is also a Super Symbolically Pertinent Rune: it's basically a way of saying (almost directly, but not quite) that there is nothing to fear but fear itself.
What other Runes do you think Clary can create? What are her limits? Why not just create a Rune of Good Guys Win and call it a day?