At the start of the game, Jack (the character controlled by the player) is a passenger on a plane that goes down in the Atlantic Ocean in 1960, after ordered society in Rapture has collapsed. After surfacing, Jack finds himself the only survivor of the crash, and swims to a nearby lighthouse, where he finds a bathysphere which he uses to descend into the ocean and enter 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 (though he's not sure which government), 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 a special plasmid that will kill only the embedded slugs while leaving the girls alive and restoring their humanity, albeit with a much smaller reward of ADAM for Jack. Tennenbaum 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 Jack and Atlas reach the bay where it is located, Ryan has it destroyed; 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 a mere two years ago, genetically modified to mature rapidly. He is Ryan's illegitimate son by an affair with Jasmine Jolene, an exotic dancer. Ryan further reveals that, after purchasing Jack's embryo, Frank Fontaine designed him to obey orders that are preceded or followed 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 Atlas and Ryan reached a stalemate, Jack was sent instructions to board a flight with a package. At a designated 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 forcing him to follow his commands 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 Frank Fontaine, having faked his own death and adopted the alias and persona of Atlas to throw Ryan off his trail. With Ryan dead, Fontaine no longer needs Jack, and leaves him at the mercy of the reactivated security systems. Nevertheless, 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 diving suit 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. Jack and Fontaine battle, and Jack eventually prevails, allowing the Little Sisters to subdue Fontaine, by swarming over Fontaine and stabbing him with their needles, killing him by draining all the ADAM out of his system. Here the game ends.
Three endings are possible depending on how the player interacted with the Little Sisters, all narrated by Dr. Tennenbaum. If the player rescued all the Little Sisters (therefore saving their lives), the ending shows the rescued Little Sisters returning to the surface with Jack and living full lives under his care, including them 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 of the adult Little Sisters. If the player harvested (and therefore killed) more than two, but not 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. Tennenbaum's voice narrates what occurred, condemning Jack and his actions. Later in the second ending, a ballistic missile submarine carrying a nuclear missile 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 harvested all of the Little Sisters, the player is shown the same movie as the second ending, though the tone of Tennenbaum's voice is angrier.