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).

If you have any other interpretation of this, I'd be glad to hear it.

Definitely relating to ME3 it seems, it reminds me of The Matrix: Path of Neo final boss and ending after The Matrix Revolutions controversy.

Here's a bit more on the subject http://www.rockpapershotgun.com/2012/03/22/frozen-synapses-changed-ending-a-mass-indie-effect/

@andrew2696 said:

Here's a bit more on the subject http://www.rockpapershotgun.com/2012/03/22/frozen-synapses-changed-ending-a-mass-indie-effect/

Ahh, didn't catch that one. I'm subscribed to RPS, but have fallen a few days behind on their articles.