Episode One begins on December 31, 1958. Elizabeth asks the private investigator
Booker DeWitt to investigate the disappearance of a young girl named Sally; Booker believes Sally is dead, but Elizabeth says she has information to the contrary. The pair confront the artist
Sander Cohen, who tells them Sally is in the Fontaine Department Store. The store was sunk and cut off from the rest of the city by Rapture's founder
Andrew Ryan to serve as a prison for the followers of his believed-dead competitor, Frank Fontaine. Within Fontaine's, Booker and Elizabeth look for Sally, fighting their way through the crazed remains of Fontaine's followers. Booker finds Sally, but discovers she has been turned into a "Little Sister"—a mentally conditioned and mutated girl, trained to produce and gather the material that fuels Rapture's genetic modifications. Booker has sudden flashbacks to events he had previously forgotten. Booker once went by the name
Zachary Hale Comstock, and was the founder of the floating city of Columbia. Childless, Comstock enlisted the help of the scientists
Robert and Rosalind Lutece to steal the infant Anna (who would grow up to be Elizabeth) from a version of Booker DeWitt in an alternate universe, but Anna was accidentally killed. Comstock was shamed by his actions and had the Lutece twins send him to Rapture, where he lost his memories and reassumed his identity as Booker Dewitt. Realizing what he has done, he tries to apologize to Elizabeth, but she rebuffs him, and Comstock is killed by an armored
Big Daddy. In
Episode Two, Elizabeth wakes up from a nightmare of Paris in flames to find herself and Sally captured by
Atlas (Frank Fontaine in disguise). A vision of Booker instructs Elizabeth to say that she knows how to get Atlas and his followers back to the city proper. Atlas agrees to hand over Sally in exchange. Elizabeth finds her own dead body, and realizes she had been killed by a Big Daddy; in returning to a universe where she died, all other alternate versions of herself have collapsed. Elizabeth has lost her previous ability to see through the
multiverse and is unsure of why she decided to return to Rapture. In the lab of scientist Yi Suchong, Elizabeth finds a portal to Columbia. Elizabeth hypothesizes that by acquiring some of the particles that keep Columbia afloat, she can lift Fontaine's building. She discovers that Suchong and Columbia industrialist
Jeremiah Fink had shared technology, co-developing the Big Daddies and Elizabeth's former warden,
the Songbird. Returning to the Fontaine building, Elizabeth succeeds in raising the department store, but Atlas reneges on their deal. After a botched attempt to drug her and learn the location of an "ace in the hole" Suchong had developed for Fontaine, Elizabeth awakens weeks later and finds the city beset by civil war. After Atlas threatens to torture Sally, Elizabeth agrees to retrieve the ace from Suchong's lab. Elizabeth finds Suchong as he is killed by a Big Daddy for harming a Little Sister. With him is a coded message that Elizabeth realizes is the ace in the hole—the phrase "would you kindly", a trigger phrase that Suchong implanted in Jack (the protagonist from
BioShock), the son of Ryan that Atlas has sent to the surface. Atlas orders his men to make arrangements for Jack to come to Rapture, and then beats Elizabeth to death with a wrench. In her final moments, Elizabeth has a vision of the events that will come to pass: Jack comes to Rapture, kills Ryan and Atlas, and saves Sally and the other Little Sisters. A post-credits scene shows a shot of Rapture as a crashed plane sinks into the city, signaling Jack's arrival and the events of
BioShock. ==Development==