After The Battle of the Wounded Knee, Booker DeWitt was overcome with guilt for the atrocities he committed, and, so, sought a way to absolve himself of his sins. Coming across Preacher Witting, Booker was offered a chance to be reborn as a different man, and start anew, free of his past crimes.
In one reality, he found himself unable to go through with the baptism. However, in an alternate reality he accepted it, taking on the name Zachary Hale Comstock. After the baptism, Comstock is visited by an archangel of God named Columbia (Who is believed to be an alternate version of Elizabeth). Her visit causes him to believe that he was a prophet, and she tells him to create a floating city which she claimed would usher the world into righteousness.
He began to see the American way as the "New Eden," and the founding fathers as prophets to God's great plan. However, he also viewed the white man as the the true free race, and saw the minority races with contempt, believing them as little more than animals. He viewed Abraham Lincoln as the "Great Apostate," who brought nothing but war and death among the country.
In time, Comstock met quantum physicist Rosalind Lutece, and with her help, and the cooperation of the United States government, he was able to make the floating city a reality, naming it Columbia and creating an all white leadership called The Founders, with himself as the leader. Columbia became a symbol of American ideals, as the country was becoming a world power, and was dispatched to different parts of the world where it would be marveled by people throughout the world.
When the Boxer Rebellion in China occurred, Comstock discovered that the Chinese were holding American citizens hostage. Upon this discovery, Comstock ordered Columbia to open fire on the Chinese populace, considering them an enemy to American ideals. This act revealed to the world that Columbia was, in fact, a giant warship. The United States disavowed Columbia, and seeing this as a betrayal, Comstock seceded Columbia from the United States, and the city disappeared into the skies. From then on, Comstock considered Columbia the true America, believing the old America to be a husk of what it once was.
Over time, Rosalind Lutece found through experimentation of the quantum atom that she was able create a portal into an alternate universe, meeting an alternate version of herself, Robert Lutece, whom she quickly befriended, and began calling him her "twin." She reported her findings to Comstock. Upon this discovery, Comstock gave Rosalind the task of finding a way to create a tear that would allow passage into these holes. With the help of Robert, the two were able to create a machine to perform the task. Utilizing this machine, Comstock claimed to see into the future, having the citizens believe he was the true prophet of God. This also allowed Columbia to become more technologically advanced, with Jeremiah Fink helping to mass produce the technologies discovered through use of the machine.
However, Comstock soon discovered that using the contraption caused his body to deteriorate, causing him to age faster and rendering himself sterile. Desperate to carry his seed into the future, he decided to obtain a child from an alternate reality. The Luteces seek out and find Booker, offering to wipe away his debts if they give him his daughter, Anna DeWitt. Booker agreed, giving Anna to Robert, who brought her to Comstock.
Booker almost immediately regretted the decision, tracking down Robert. He finds them in an alleyway preparing to pass through a tear back to Comstock's dimension. He tries to stop Comstock from going through, but he manages to escape. However, the tear closes a moment too soon, slicing a portion of Anna's little finger off. Because a part of her body exists in another universe, Anna would later have an intuitive ability to manipulate the forces the Luteces brought to Columbia.[citation needed]
Seeing Anna as the key to making his dream of remaking the world a reality, he created Monument Island to house her, where she, after being experimented on, acquired her powers to create Tears-portals through dimensional space and time-but Comstock saw to the creation of the Siphon, which limited her powers.
Comstock used these inter-dimensional abilities with the siphon to create a guardian creature known as the Songbird, which would not only keep her safe, but also prevent her from escaping. Renaming her Elizabeth, Comstock began to call her the "Lamb of Columbia," and the Founders soon worshiped her as a savior.
Unfortunately for Comstock, overuse of Rosalind and Robert's contraption not only caused him to get cancer, but also gave him knowledge that Elizabeth's real father would eventually find a way to take her from him. He warned the populace that a "False Shepherd," would appear, bearing the mark "AD" on his right hand-which was what Booker branded on his own right hand-and became determined to turn Elizabeth into a version of himself.
However, Lady Comstock was growing more and more frustrated and angry with keeping the truth about Elizabeth from the populace. Knowing that she was going to break, Comstock had her killed, and framed his servant Daisy Fitzroy for her murder. Daisy would later become the leader of the Vox Populi. Soon afterwards, Rosalind and Robert had seen, through tears, the future of Columbia and what Elizabeth would soon become, and they planned to send Elizabeth back to her original universe in order to prevent that future from happening. However, Comstock soon discovered what they were doing, and ordered Jeremiah Fink to sabotage their contraption, apparently killing the two as they were using it.
In actuality, the sabotage caused Rosalind and Robert to exist across all space and time, giving them the ability to appear wherever, and whenever they wanted. Still determined to stop Comstock, they devised a plan to send Booker DeWitt into Comstock's universe in order for him to retrieve his long lost daughter. The process of crossing realities caused Booker to lose much of his memory about Comstock and Anna. The only part he remembered was Robert telling him "Bring us the girl and wipe away the debt," which ultimately makes him believe that he is retrieving Elizabeth from Columbia and bringing her to New York to pay off his gambling debts. And, so, Booker ascends to Columbia to rescue Elizabeth.
Comstock sends the Founders after Booker, determined to stop him from taking Elizabeth. He even uses Elizabeth's powers at one point to create a version of Lady Comstock that is both living and dead in order to stop them from proceeding. But, an older Elizabeth, feeling regret that she allowed herself to become Comstock's heir-the executor of his desire to "drown in flame the mountains of man"-brings Booker to her universe after the Songbird captures the young Elizabeth, and gives him a note that will show her younger self how to avoid her fate, and, later, Booker is able to free Elizabeth from Comstock.
Determined to put an end to the evil of Comstock, Booker and Elizabeth board his ship, The Hand of the Prophet, and confront him in his cabin. There, Comstock shows remorse, wondering why he did not tell the truth to Elizabeth, and, instead, sent his armies after her and Booker. He grabs Elizabeth and demands Booker to tell her the truth of how she lost her finger. Booker kills him in a rage.
Destroying the siphon at Monument Island, Elizabeth is able to unlock the full extent of her powers. Using them, Booker remembers what he had done, and the two travel to the place of Booker's baptism after after the Battle of Wounded Knee (which he refused to go through with in his own universe). Booker and Elizabeth discover that an alternate Booker's acceptance of the baptism resulted in him being "reborn" as Zachary Comstock, meaning that Booker and Comstock were one and the same-Elizabeth reveals that, in order to truly destroy Comstock, throughout all the realities he exists in, Booker would have to die before his alternate self could take the baptism.
With this revelation, Booker allows a number of Elizabeths from different universes to drown him. Because of this, Comstock, and all the events that took place in the game, are erased completely from existence.
