I saw on the Steam patch notes that Frozen Synapse has "a brand new ending for a limited time only". Unless this is an early April Fool's joke, I'm assuming this new ending is related to people asking that Mass Effect 3's ending be changed. Note that the rest of the post contains Frozen Synapse spoilers (but not Mass Effect 3 spoilers).
The original ending:
The new ending:
If you have any other interpretation of this, I'd be glad to hear it.