Cassie Clare talks about the relationship between Sebastian and Clary

Cassie Clare shared some explanation about the relationship of our fave villian Sebastian Verlac aka Jonathan Morgenstern. Don't read on if you haven't read City of Lost Souls. 

of Sebastian and Clary
Hi Cassie, first I love your books and I can’t wait for CoHF to come out, even though I’m kind of scare that it might break my heart, anyways, I don’t know if you’ve already answered this question ( sorry if you have) but can you please help me to better understand Jonathan/Sebastian’s feelings or non feelings or whatever his deal is towards Clary? Or is it going to be better explained in CoHF? Thanks! — racheltavarez18 

Jonathan/Sebastian’s relationship with and feelings toward Clary are complicated. Part of the reason they are not just explicit on the page “Jonathan looked at Clary, and realized that he loved her as a sister/hated her as an enemy/loved her the way you love a pet frog and did not have any other feelings or any conflicting emotions as regarded her” is because Sebastian is himself working through what he feels about Clary. (Also because no one actually thinks that way.)
Ideally, all characters have complicated emotions about other characters. Alec loves Jace like a brother, but he did once have a crush on him, and he also is sometimes jealous of him for getting all the attention, and he feels protective of him but also is driven to distraction by his self-destructiveness and recklessness. Even positive emotions are complicated.
Sebastian is a character who has a very uneasy relationship with emotions at all. He was probably attached to Valentine. He got very upset at the idea that Valentine might have cared about Jace. He doesn’t really think of himself as someone who can love but he gets annoyed when people don’t love him. He actually goes on at great length in City of Lost Souls to Clary about what he thinks he feels about her (“You know, when I first met you, in Idris, I had hopes—I had thought you would be like me. And when you were nothing like me, I hated you. And then, when I was brought back, and Jace told me what you did, I realized that I had been wrong. You are like me” — etc. pg 361) , and then she explains to Jace in the end what she thinks Sebastian feels about her. (“Loneliness drove him as much as a desire for power—loneliness and a need to be loved without any corresponding understanding that love was something you earned. “)
Now you don’t necessarily have to believe Sebastian when he talks about his feelings, and you could think Clary is wrong. Or I guess you could be looking for something really explicit and categorizable — “He loved her as a frequent traveler loved a rolling suitcase” — but sometimes the thing is that the characters don’t necessarily understand or want to comprehend their own emotions explicitly because they are in the process of coming to understand them. Think of Harry and Snape — how Snape actually felt about Harry was somewhat baffling right up to the end of the Harry Potter series because the development of Snape’s relationship towards our protagonist is, in fact, his character arc. You cannot just be told it up front. That would wreck the story.
So I guess the answer is that you really need to read to the end of the series to get the clear picture of how Sebastian feels about Clary because again, how this particular character feels about the protagonist is his character arc. I don’t think my explaining it would be a good idea further than it has already been explained in the books — I wouldn’t have been all that happy with someone who had handed me a card that said SNAPE HAS COMPLICATED FEELINGS ABOUT HARRY BECAUSE HE WAS IN LOVE WITH HIS DEAD MOM before Deathly Hallows came out. (Though, admittedly, I had guessed. But I still prefer the journey on the page, and therefore I inflict it on you!)

You can read more about Sebastian in this outtake from City of Glass. Go here to read it.