The Prototype 2 trailer after the break helps explain why Prototype 1 protagonist Alex Mercer is the bad guy in this sequel ... but we don't think it needs all that much justification. He was always a mass-murdering monster; he just happened to be the monster in the player's control before. It's like Godzilla movies -- sometimes he's the bad guy, and sometimes another monster will be tearing up Tokyo and Godzilla becomes the hero by default.
After the narrative discussion, the trailer treats us to a little footage labeled "Pre-alpha." Luckily, Activision remembered to use that term instead of "Prototype," because that would be so confusing.