SPOILER ALERT BELOW, NOT ABOVE

~City of Bones: Kidnapped by Valentine, also finding out Clary is his sister although that applies to both of them.
~City of Ashes: Not really anything except having to deal with Clary being his sister.
~City of Glass: goes after Sebastian and almost gets killed, actually does die.
~City of Fallen Angels: Is controlled by Lilith
~City of Lost Souls: Is controlled by Sebastian, Clary plunges Glorious into his chest.
~City of Heavenly Fire: The whole deal with Sebastian, but that applies to most main characters.

TMI fandom!