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Fontaine/Atlas had you fast grown from a bastard child of Andrew Ryan (this is why only you can use the Vita chambers in rapture because atlas set them to only work for him and his family (you)), you were conditioned to obey any order with the phrase "would you kindly". fontaine and ryan were rivals to control Rapture. You were sent out of Rapture as a sleeper agent while rapture f*cked itself over in its civil war. Then you were sent back to Rapture, forced to crash the plane you were on into the sea and then Atlas uses you to overthrow Ryan and let Fontaine control Rapture.