If anybody is having trouble with this, you have to euthanize the whale in the factory and then take the eye on the side that faces the factory floor. The weeper you need is in the alley where you have to rescue your assassin from the music box overseer.

I was looking for the eye after i kill the whale, but i couldn't find it anywhere. Guess i will try harder next time.

It's still inside the whale.

http://www.youtube.com/watch?v=MXWnwQwlXQA

Can be a little confusing

What does the weeping eye do?

It just gives you a rune. Which was kind of disappointing, but eh.