I killed the Unseeing eye (my fire elemental tore it to shreds ) Right after the Unseeing eye apeared i got one of those little things over my head saying i should use the rod on the unseeing eye. So i did and the rod killed it and then disapeared. I went and killed Gaal and everyone and i checked EVERYWHERE but i cant find the rod....so i cant complete the quest. does anyone know where the rod went?

If you used the rod to kill the Elder Orb, then it should disappear from your quickslot into your inventory. you should then go back to the abandoned temple where you got the part of the rod, this will complete the quest.