No, it's not some kind of commentary on BioWare and the controversy surrounding Mass Effect 3's ending -- this is an experiment, an altered ending for Frozen Synapse that will live for a limited time. "This wasn't intended as a criticism of Bioware," Frozen Synapse developer Mode 7's Managing Director, Paul Taylor, told Joystiq. "I thought it would be interesting to take a load of fan suggestions and then just make the worst ending I could imagine; a kind of horribly self-referential meme-laden nightmare, and then just slap that on the game for a week and see if anyone cared."
One player already grabbed video of the altered ending, which you can see embedded above. "The thing that's interested me most about doing that is that people (mostly) seem to get the joke and also seem to want to use it as a starting point for a conversation about stories in games." We'll just have to take his word for it -- we'll never be smart enough to play Frozen Synapse.