Fortunately, at the end of a recent Mass Effect 2 dev blog post, the game's executive producer, Casey Hudson, responded to the notion of Shepard's corpsification, saying he "better not be." He continued, "we had a lot of big plans made, so if someone's gone and killed Shepard then things are going to take an unexpected turn." So, there you have it. Either Shepard is still alive, or some unknown, shadowy agent murdered him without Bioware's noticing. Either way, we should know more about Shepard's status when we see the game next month at E3.
