<P> Clary learns that Valentine Morgenstern , the main antagonist of the series , is her biological father and her mother 's ex-husband . At the end of City of Bones , Valentine tells them that Clary and Jace are siblings -- which , they discover later in the series , is a lie . In the second book of the series , City of Ashes , Clary dates her best friend Simon , who has for a long time had a crush on her , in order to forget Jace during the torturous time of believing him to be her brother . She is told by the Seelie Queen that she has the ability to create runes that do n't exist ; but they do exist , which later enables her to destroy Valentine 's ship using the `` Open '' rune . In the end of the second novel , Clary finds that an old friend of her mother , Madeleine , knows how to wake her mother , who has been in a magical coma since the first book . </P>
when do jace and clary find out they are siblings
At the end of City of Bones