Sadly, Irrational's (oops, I meant 2K Boston) latest FPS and contender for GOTY has to come to an end sometime. Players start off controlling an unnamed protagonist who somehow survived a plane crash. A lone lighthouse nearby leads the way down to a strange submarine like contraption. Boarding the submarine, players find themselves entering the eerie world of Rapture. A stranger's voice comes out over the radio, asking if you would kindly help him get back to his family.
Throughout the first half of the game, the character has flashbacks. Brief glimpses of a family photo, a house, a life before. With the help of Atlas who keeps contact over the radio, you navigate through Rapture, trying to reunite him with his family and at the same time, trying to figure out what the heck is going on.
[The mysteries of rapture after the cut. Spoilers ahead!]
The short version: You're Andrew Ryan's son, Fontaine is Atlas, Fontaine brainwashed you to do his bidding, you kill Fontaine, you get back to the surface.
The long version:
You find out that Rapture is the brainchild of Andrew Ryan. He wanted to build an underwater utopia free from religious and governmental control. Unfortunately, his utopia turned into a dystopia thanks to his projects in genetic modification. People became so obsessed with modifying themselves (splicing) that they slowly lost their humanity.
At the same time, a war was raging in Rapture. Fontaine versus Ryan. Both sides had spliced armies. The city was destroyed; only the spliced people remained.
This is where you, Jack, come in. You thought you were helping a man, Atlas, get back to his family, but it turns out Fontaine is just pretending to be someone named Atlas to get you to sympathize with him and follows his orders.
Some time ago, Fontaine devised a plan to bring Ryan to his downfall. He and Tennenbaum (a brilliant scientist leftover from WWII), paid a dancer at a nightclub to sleep with Ryan and get pregnant. They bought the child. When Ryan found out, he killed the dancer.
The child, who had a little of Ryan's DNA would be the only one other than Ryan who could be revived through the vitachambers and use the bathyspheres to go around Rapture, which was the reason Fontaine wanted the child to exist. With the help of Suchong, who accelerated the child's growth into a man, Fontaine brainwashed the child and implanted fake memories of living on the surface and having a family. That's how you, Jack, came about.
When Jack finally meets Ryan, Ryan expresses some pity, calling his son his greatest disappointment. He tells Jack that a man chooses, a slave obeys. Basically, Jack is Fontaine's slave. To illustrate the point, Ryan orders Jack to kill and beyond Jack's control, he kills Ryan.
Having no more use for Jack, Fontaine tries to destroy him. But Tennenbaum saves him and has Little Sisters lead him into the nursery where Jack was born. Tennenbaum tells Jack how to free himself from Fontaine's control with some antidote in Suchong's office.
After Jack frees himself, he goes and takes on Fontaine, who ends up being some grotesque spliced up man. Jack drains most of Fontaine's EVE, and the Little Sisters help and take the rest.
If you saved the Little Sisters throughout the game, the good ending has you saving them and bringing them up to the surface. They live a normal life and your reward is their gratitude to you.
If you harvested the Little Sisters, you get the bad ending, which has you taking a bathysphere up to the surface and attacking some people who are checking out the wreckage. It turns out that you've turned into a splicer yourself.