She was neglected, underestimated and looked down upon. Even Jace and Isabelle who seemed to have the most faith in her told her to just give up 'cause maybe she didn't have it in her.
Nothing pisses her off than being told what she can and can't do. She leaves for years, moving to Japan where her brother and father are, impossible to track, impossible to reach.
Three years pass and everyone moves on with their lives; Jace even manages to get himself a new love interest, but then a tragedy happens.
While the New York shadowhunters are at a field trip in Idris, demons invade New York and leave the Institute and their school Accords Academy in ashes. All the other Academies are full and can't accommodate their numbers, except for the one in Japan where Valentine Morgenstern along with his son, Sebastian, known as the best shadowhunters of their time, reside. Who, also happen to be Clary's father and brother.
While their stay in Japan, demons grow stronger and smarter and are coming in through deathly numbers. The Clave has no choice but to form an army composed of the best of the best of not only Nephilim, but downworlders as well.
Jace, Clary, Simon, Isabelle, Alec, Magnus, Jordan, and Maia are among the chosen warriors, along with Sebastian and his friends, Kazuma, Dylan and other selected Nephilim. Valentine is tasked as their trainer and commander.
But when training starts, they are shocked to say the least at the transformation of a certain redhead, and only one question crusades their minds.
Who are you and what have you done to Clary?
"Jace you have to understand that leaving-"
"You had a choice. You had a choice and you chose the Clave. You chose the Clave over the people who took you in when you needed it the most."
"That's no fair Jace. You and I both know that there's no telling the Clave no."
"They gave you time to say goodbye and you ran in the middle of the night. You always run. You ran from us and from Valentine. And you run away from your feelings."
Emery left before the war, working with the Clave. After the war she returns back to the New York Institution to her family.