I was going to say I thought you may have mixed up a couple of stories! I'm glad you got one sorted out. I believe the second (Jared turning a city to metal) is Naked Under Here (http://fleshflutter.livejournal.com/158348.html) by fleshflutter, but it's not a big part of the story, but rather part of the backstory.

Do you have a link to the one where Jensen is kidnapped by an ex? I can't recall if I've read it.

I also second the recs list from the first comment, and also want to add a rec for The Jolly Roger (http://archiveofourown.org/works/1994493/chapters/4320768). Take heed of the warnings, in case it's not your thing, but a great story about superpowers in a slave-driven society.