There are two major things that happen during the last chapter of City of Bones and they're not good:
(1) Valentine escapes with the Mortal Cup. Um, dang. Clary and friends spend the majority of the book trying to get this magical goblet back, and they lose it in the end. Bummer.
(2) Clary and Jace find out they're brother and sister. Um, double dang. Not only is Jace one of the hottest guys Clary has even laid eyes on, but they kind of kissed. A few times. Bummer doesn't even begin to describe it.
With those two things in mind, this could end on a major low note. But Clare includes an epilogue that makes things a little more upbeat.
The Epilogue is called "The Ascent Beckons" so that clues us in that things will get a little sunnier. Thankfully, they don't get too sunny, because the primary action in the epilogue involves Jace taking Clary on another bio-bike ride, and those things are severely allergic to sunlight.
Anyway, Jace takes Clary out over the city in the final scene of the book. This time, she doesn't cower in fear. She keeps her eyes open and soaks it all up. Despite all the deaths and near-deaths she's seen, she doesn't want to go back to the way she saw the world before.
Although we think she'd make an exception if she could rewind to the part right before she found out this handsome hunk was a blood relation. Awkward.