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Clary's mother has been hospitalized in a comatose-like state for over three days, while Clary visits her every day.
After visiting hours, Simon takes Clary back to the Institute, where he gives her a small kiss before letting her out of the van.
At the Institute, Clary runs into Isabelle, whom Jace has selectively filled in on a few details. For example, she knows that Hodge had his curse removed and left, but she doesn't know that he was a giant honking traitor.
Also, Alec survived the attack from Abbadon and was nursed back to health by Magnus Bane.
Alec takes Clary up to the greenhouse, where Jace is, and apologizes for the way he treated her.
It seems that Jace has taken the whole evil-father thing pretty hard. He also feels sorry for Hodge, and kind of wishes he had gone through the Portal to Idris, the only place where he ever felt happy.
He looks in the Portal shard every once in a while, watching Idris and hoping to catch a glimpse of his father.
At the very end, Jace leads Clary to the roof of the Institute, where a new hijacked flying bio-bike is waiting.
He takes Clary on a beautiful trip across New York City.
Even though it's pretty gosh darn scary, Clary "kept her eyes open, so that she could see it all" (Epilogue.176).