@DDUU11: Well from what I've seen so far, the scientist was probably killed by the Queen after the Oystercloud experiment was completed. My guess for the Oystercloud project would be that the Queen wanted to get into our world somehow? (Probably merge them together and rule both worlds or something...) If you checked out the terminals at Episode 2 and read the journals and tapes in this ep, they hint more abt the reason for the project. If not, check out DAnox's post: http://www.freegamesnews.com/en/?p=18535&cpage=1#comment-340269.
I don't want to be a spoiler but that creepy crossdresser who killed was probably the 'Queen'.
 "Alice is Dead Episode 3"){kind=icon}
 "Papa's Freezeria"){kind=icon}