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I read this book back in middle school and I've been trying to remember more about it and possibly read it again.
I remember the cover was a greenish blue. It would have been around the 2004-2005 time frame. I remember the whole book had an overall dark and industrial dystopia feeling to it.
From what I remember, the book's main character was an orphan and imprisoned in a large orphanage where the kids where forced to work. There was some sort of accident during a routine transfer and he escaped with some other kids. These other kids ended up fighting a government-type military who was trying to capture them... there was also something to do with a creature or aliens.
I want to say it started with a "C".