a very similar story, you would like it
if you liked City of Ember, you would like this book:
http://en.wikipedia.org/wiki/Orphans_of_the_Sky
It might sound different at first, because it's in outer space, but the basic idea is almost identical to C.o.E. A gigantic spaceship is launched, to explore a nearby star. It has thousands of crew members on board, and they all understand, when they get on board, that the flight is expected to last for many generations. As time passes, there is some sort of mutiny, and subsequent generations grow up with no real understanding of the fact that they live in an artificial spaceship... it is just "the universe" to them. A few young people figure out the true nature of their environment, and... it's quite similar to C.o.E.
Who's... laughing... NOW?!? BZZZZZZ (hack hack spurt spurt) HA HA HAAA BZZZZZ HA HA HAAA