Story

Jack is a passenger on a plane that crashes over the Atlantic Ocean in 1960, after ordered society in Rapture has collapsed. After surfacing, Jack swims to a nearby lighthouse, where he finds a bathysphere in which descends into the ocean and enters the failed "paradise" of Rapture. Atlas assists Jack via radio in making his way to safety, while Ryan, believing Jack to be a government agent, uses Rapture's automated systems and his pheromone-controlled Splicers against him. Atlas tells Jack that the only way he can survive is to use the abilities granted by plasmids, and that he must kill the Little Sisters to extract their ADAM. Overhearing Atlas' words, Dr. Tennenbaum intercepts Jack, and urges him to save the Little Sisters instead. She gives him the means to only kill the embedded slugs while leaving the girls alive and promises to repay him if he does as she asks. As Jack works his way through the city, he learns about Rapture's fate and history through audio logs, genetically-induced ghostly playbacks of past events, and radio messages. Atlas says his wife and child have been hiding on a submarine, and just as they are about to reach their goal, Ryan has it detonated; an enraged Atlas tells Jack that Ryan must die.

Jack makes his way to Ryan, who offers no resistance to Jack's efforts, but instead reveals why Jack has come to Rapture: Jack was actually born in Rapture two years ago, genetically modified to mature rapidly; he is Ryan's illegitimate son as a result of an affair with Jasmine Jolene, an exotic dancer. Ryan further informs Jack that he was designed to obey orders when given with specific phrases, then sent to the surface when the war started to put him beyond Ryan's reach. When the conflict between Atlas and Ryan reached a stalemate, Jack was sent instructions with the result that he boarded the flight with the package. At a pre-appointed time he opened the package to discover a gun and instructions to hijack and crash the plane next to the lighthouse, enabling him to return to Rapture - as the cat's-paw of Atlas. Ryan calmly demonstrates Jack's lack of free will by using the trigger phrase, "Would you kindly...", which Jack then realizes Atlas has been using since his arrival. Ryan then orders Jack to kill him, so as to die on his own terms. Atlas, in complete control of the city as a result of Ryan's death, reveals himself to be Fontaine. With Ryan dead, Fontaine no longer needs Jack, and leaves him at the mercy of the reactivated security systems. However, Dr. Tennenbaum and her Little Sisters help Jack escape through the vent system, where he falls and loses consciousness.

When Jack awakes, Dr. Tennenbaum has already deactivated some of his conditioned responses and assists him in breaking the remaining ones, among them one that would have eventually stopped his heart. During their subsequent pursuit of Fontaine, the doctor predicts that the only way to get through the last few obstacles would be to assemble a Big Daddy bodysuit, and follow the rescued Little Sisters through the passageways that only they can open. By the time Jack reaches him, Fontaine has injected himself with vast amounts of ADAM, becoming an inhuman monster that resembles the famous bronze statue of Atlas. Jack and the Little Sisters are eventually able to subdue Fontaine, when the Little Sisters swarm over Fontaine and stab him to death with their ADAM needles. Here the game ends.

Two endings are possible depending on how the player interacted with the Little Sisters. If the player only rescued the Little Sisters (therefore saving their lives), the ending shows the rescued Little Sisters returning to the surface and living full lives under Jack's care; it ends on a heart-warming tone, with an elderly Jack surrounded on his deathbed by all of the adult Little Sisters. If the player harvested (and therefore killed) any of the Little Sisters, the game ends with Jack turning on the Sisters after defeating Fontaine, presumably killing them all and taking their ADAM. Tennenbaum's voice narrates what occurred, condemning Jack and his actions. Later in the second ending, a ballistic missile submarine comes across the wreckage of the plane and is surrounded by bathyspheres containing Splicers. The Splicers board the submarine, eradicate all on board, and recover what appear to be nuclear weapons. If the player harvested all of the Little Sisters, the tone of Tennenbaum's voice in the second ending becomes a bit more angry.