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Shortly after the middle of the game, it is revealed that Jack is the illegitimate son of Andrew Ryan and Jasmine Jolene. This fact and other Audio Diaries explains how the Vita-Chambers work on Jack and not splicers.

An Audio Diary by Jasmine Jolene (Pregnancy), Ryan's mistress, and photos found on Ryan's desk indicate that Jack was purchased by Bridgette Tenenbaum on behalf of Frank Fontaine as an embryo. When Andrew Ryan discovers this arrangement he kills Jasmine. Andrew Ryan's shoes and pipe are found at the scene, and Jack can smoke his father's pipe with the same effects as cigarettes. This is one of only two pipes found in the game.

On Jack's wrists are tattoos of some chain links. This could be a reference to Andrew Ryan's "Great Chain" or more likely that it is symbolic of Jack's enslavement. The tattoos could also be explained as a reference to Dagny Taggart's chain link bracelet in Ayn Rand's Atlas Shrugged. (Note: the chain links on the right wrist are visible during the cutscene where the first plasmid is acquired, and when the player is wielding the wrench.)

Jack was raised by the scientists in Rapture who were responsible for his mental conditioning at the order of Frank Fontaine for the purpose of assassinating Andrew Ryan. According to Audio Diaries by Dr. Suchong, who was responsible for Jack's development, Jack weighed 56 pounds and had the "gross musculature of a 19 year old by the age of one". Dr. Suchong also reveals in another Audio Diary that he is responsible raising Jack and the mind control imprinting that Frank Fontaine requested. Jack is sent to the surface as a sleeper agent living in his pre-programmed life until Frank Fontaine 'activates' him. Upon Fontaine's command, Jack boards a plane that passes over Rapture's entrance, then hijacks it, forcing its crash landing, using the trigger phrase "Would you kindly".

Jack eventually finds a cure for the conditioning with the help of Bridgette Tenenbaum, a chemical produced by Dr. Suchong called Lot 192. Jack completely frees himself from Fontaine's mind control. Once free, Fontaine challenges Jack to a showdown. In order to pursue Fontaine, Jack is forced to become a Big Daddy however, this transformation is not complete, as he does not have the suit grafted onto him (he never wears the gloves either), nor is his mind altered in the process. Afterwards, Jack confronts Fontaine and finally kills him with the aid of Little Sisters. Depending on the player's actions throughout the game Jack will either become the new ruler of Rapture and leader of the splicers or he escapes to the surface with the Little Sisters, raising them as his own daughters until dying of old age.

While Jack's face is never directly seen in the game or in cinematic cutscenes (both of which take place largely in the first person perspective), a few pictures of him can be found throughout Rapture. His voice is heard twice, in the beginning cinematic and in the Mind Control Test audio diary.

Taking his biological father into account names the character Jack Ryan, a character created by Tom Clancy with whom he shares some thematic aspects: Both have an "everyman" quality about them, that of a tough but relatively normal person thrown into circumstances for which they are psychologically unprepared. Andrew Ryan initially suspects that Jack is a CIA spook, then comes to the conclusion that he is not based on his behavior. In contrast, Clancy's Jack Ryan actually is a CIA employee whose mission requires him to impersonate a naval officer. Both are forced to engage in gun-play underwater to survive.