The narrative of the song is about a scientist commissioned to deconstruct/disassemble a female humanoid robot. In the process of taking her apart he falls in love with her and afterwards regrets what he's done. But, is it too late to put her back together again? Listen to the song to find out!
The idea behind the lyrics is twofold. Firstly, it's loosely based on the idea of the Uncanny Valley, which conerns man's emotional response to robots. The theory goes that, as robots become ever more lifelike, our emotional response to them will turn from postitive ("Wow, it looks so real!") to outright revulsion ("Oh, the humanity!"). However, as robots grow even closer to mimicking humans, our response will shift back to being positive ("Aw, how could I have hated someone so cute?"). This sharp dip and ensuing rise in positivity is the theory's 'valley'.
You can read all about it here: http://en.wikipedia.org/wiki/Uncanny_valley
Ultimately though, the song is about irreparably destroying something you love and the ensuing regret.