Eventually, after completing tasks throughout Rapture (like saving an artificial forest from dying and helping an insane artist build his sculpture), Jack confronts Ryan, who is casually playing golf in his office. Ryan reveals a truth that he has pieced together: Jack was actually born in Rapture just two years ago, genetically modified to mature rapidly. He is Ryan's illegitimate son by an affair with Jasmine Jolene, a dancer. When Jolene became pregnant with Jack, she (in desperate need of money) had her embryo surgically removed and sold it to the highest bidder. She had not realized it was Frank Fontaine who purchased the son, leading to her death by an enraged Ryan. Ryan further reveals that, after purchasing Jack's embryo, Fontaine designed him to obey orders that are preceded by the specific phrase "Would you kindly...". Jack was then sent to the surface when the war started to put him beyond Ryan's reach. When the conflict between Fontaine and Ryan reached a stalemate, Jack was sent instructions to board a flight with a package and to use its contents, a revolver, to hijack and crash the plane near the lighthouse, enabling him to return to Rapture as a tool of Fontaine. Because Jack was Ryan's son, he could freely use Rapture's bathysphere network, which had been locked out to everyone except those within Ryan's "genetic ballpark". Finally, Ryan has Jack kill him, wanting to die on his own terms. With Ryan's death, Jack realizes too late that Atlas has also been using the trigger phrase to control him. Atlas reveals himself as Fontaine, who faked his death to throw Ryan off his trail and take control of the city, leaving Jack at the mercy of the reactivated security systems. Dr. Tenenbaum and her Little Sisters help Jack escape through the vent system, where he falls and loses consciousness.

When Jack awakens, Dr. Tenenbaum has already deactivated some of his conditioned responses (such as the trigger phrase itself) and assists him in breaking the remaining ones, among them one that would have eventually stopped his heart. When it becomes clear to Fontaine that he is losing control of Jack, Fontaine points out the peculiar fact that Tenenbaum has survived both World War II as a Holocaust victim and the battle in Rapture, insinuating that she has a secret agenda of her own. With the help of the Little Sisters, Jack is able to track down Fontaine. Fontaine, having been cornered, injects himself with vast amounts of ADAM and becomes an inhuman monster. Jack battles Fontaine, eventually prevailing and allowing the Little Sisters to subdue and extract the ADAM from Fontaine, killing him.

Three endings are possible depending on how the player interacted with the Little Sisters, all narrated by Dr. Tenenbaum. If the player harvested no Little Sisters (thereby saving their lives), the ending shows five Little Sisters returning to the surface with Jack and living full lives under his care, including their graduating from college, getting married, and having children; it ends on a heart-warming tone, with an elderly Jack surrounded on his deathbed by all five of the adult Little Sisters.

If the player harvested (and thereby killed) all or almost all of the Little Sisters, the game ends with Jack turning on the Sisters after defeating Fontaine, presumably killing them all and taking their ADAM. Tenenbaum narrates what occurred, condemning Jack and his actions, voice thick with anger and contempt. Later in the second ending, a George Washington-class submarine carrying nuclear missiles comes across the wreckage of the plane and is suddenly surrounded by bathyspheres containing Splicers. The Splicers kill all hands aboard the submarine and take control of it.

If the player killed more than one Little Sister, but not enough to obtain the previous ending, the ending is visually identical to the second one, although the tone of Tenenbaum's voice is a sad one, as opposed to angry and there are minor dialogue changes