Question: are clary and jace going to be together?
Answer: In The Mortal Instruments, after fighting off idiotic psycopathic family members (like a psychic brother-Sebastian, and a psychic dad-Asmodeus) the Lightwood siblings, Jace and Clary return back to Alicante. But yes, Clary and Jace are together again. The Heavenly Fire is gone from Jace.