In COF; at the lake Valentine wins, Jace doesn't show up to be killed and the angel doesn't kill Valentine or give him his wish.
When Sebastian throws Clary in the lake, Valentine jumps in to save her. He heals Clary and forces her to work for him as an enforcers the followers of Valentine that control the rogues. Clary is forced to create runes, ones that give Valentine the complete power over his followers and others.
Clary's friends and family got away but it's not enough to control her fears. She's deathly afraid. If she sees them... any of them, what will stop her from turning them in or even worse killing them. She may have power over her mind, but not her body.
Valentine trains Clary to be just as good as Sebastian (Jonathan). Sebastian's Jealous. He tried to kill her once and if he ever gets the chance he'll try again.
***********When I change the end of the book so much it's hard to really explain because I end up getting reviews that say, BUT THIS HAPPENED... AND THAT HAPPENED... Ugh okay :)