I personally think the the theme was Man (humanity) vs Machine. As Cortana becomes increasingly rampant she becomes increasingly human, and in contrast the Chief has to become more machine like and hide his emotions (more than he usually does) to make sure they both don't fall apart. At the end you're not meant to be sure whether Cortana's "death" has brought Chief back to his humanity or pushed him completely over the edge into machine territory. That is what I got from it anyway...