Atlas asks you (in a kind manner) to rescue his family from a submarine located in Smuggler's Cove. When you arrive and press a button, some splicers show up and the submarine is destroyed.
Once you finish the game and realize Atlas is actually Frank Fontaine, it seems unlikely that his family was in that submarine. I did some internet research and others claim that the bodies you find around the submarine were just there to put on a show for Andrew Ryan. Why would Atlas need to put on a show for Ryan? Ryan was already out to kill Atlas, so why would this matter? Another theory is that the 'family in submarine' story was there to convince the player (Jack) to help Atlas. This is unnecessary, as you're a brain washed puppet who can be controlled by saying 'would you kindly,' so why would Atlas bother trying to convince Jack he's a good guy? Another problem with that theory is t that you (the player) might get to see inside of the submarine, and if his family wasn't inside, Atlas would have to explain to Jack why he was lying.
A theory of mine is that Atlas was going to use that submarine to escape Rapture (now, or in the future).
So, what was in the submarine?