Spoiler
You are Jack, Ryan’s son. Andrew Ryan had slept with a dancer at a night club (who was paid no to use birth control by Fontaine). The stripper had the child and gave/sold it to Fontaine and Tennenbaum. Fontaine brainwashed you and implanted false memories of a life on the surface into your mind. Suchong accelerated your growth so you were full grown. The plane crash, the “family” were all staged.
Fontaine brainwashed you to listen to his commands and pretended to be Atlus. He needed you to do his bidding to defeat Ryan because only Ryan’s DNA, which you have, can work the vitachambers and bathyspheres. You get to Ryan and he knows you’re his son. He calls you his biggest disappointment and says “a man chooses, a slave obeys.” Then he says, “KILL” and you lose control of Jack and Jack kills Ryan.
Tennenbaum tells you that you have to free yourself of Fontaine’s brainwashing, which you do thanks to some antidote that Suchong had hidden away. In the end, you kill Fontaine (who is all spliced up) and get an ending depending on whether or not you harvested the Little Sisters.
If you didn’t harvest any Little Sisters, then you end up saving them and bringing them up to the surface in a bathysphere. They go to school, grow up, get married, and visit you when you’re old and gray.
You go to the surface in your bathysphere and attack some people who were just checking out the wreckage.