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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.

SPOILERS AHEAD

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?

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The issue is that while you are blindly following Atlas' orders because he asks you oh so kindly, is that it's just a trigger. However, triggers can be broken.

The reason Atlas is attempting to put on a show for you is so that he can convince you to do his bidding.

Later in the game, when you discover what has been happening, he explains the whole "Would you kindly" situation, and you, as Jack, begin to overcome the underlying brain function that leads you to follow everything he says. The conflicting situation begins to break the bond he is controlling you with

Basically, while he is using the trigger to force you into doing what he wants you to do, how would you react if you actually did see what was in the sub? It would confuse you. It would weaken the link. He needs to convince you to hate Ryan, so that you have no reason to question him when you confront Ryan

And beat him bloody with a golf club. Fore!

So as for what was in the submarine, because we never really do get a proper look, it could be any number of things. But it likely was his plan to never use the sub in the first place.

As Atlas is Frank, he controls the splicers, much in the same way he controls you. Just it's much easier to control them, because their minds are so broken already. As for why he doesn't use them to kill Ryan, well, that's a whole other question...

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  • That's a convincing argument, so thanks for a good answer. Atlas also seems to be quite a dramatic guy, and would enjoy putting on a show.
    – DeeCeptor
    Feb 16, 2015 at 21:03
  • There's still a bit of a problem. The splicers that attacked were controlled by Ryan, not Atlas. If Atlas had misjudged Ryan, and Ryan didn't attack - or if Jack had escaped the control room and managed to fight off all the splicers - the secret would be exposed. >! Unless Atlas had rigged the sub to explode, and would have detonated it in all circumstances even if there was no visible reason. Another question would be why Atlas would put himself at risk, unless he is sufficiently good at combat that he wasn't scared of a few splicers.
    – David Szwer
    3 hours ago

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