The secret mission was a last minute addition to Silent Fury and is only very short (5-10 minutes) with no combat involved. This is how to find it:
As for how to complete all the objectives in the secret mission, well, I won't spoil that yetOn mission 3, in the first segment - not the second one with the freighter - after your first encounter with a wave of Gemini raiders, a miner appears from the asteroids.
If you use this time before the next attack you can find a container not far from where the miner appeared. It won't appear on your HUD notification as an open container which is why you may have missed it.
The container will drop a key that downloads a mission request to your ships log. You'll be given the option to accept the mission (using your inventory menu). Once you've accepted it, the details of the mission will be downloaded to your log. Be sure to review it before proceeding to the next mission (you'll be automatically sent to the secret mission after).