On Christmas Eve, Batman intervenes in a breakout at Blackgate penitentiary led by Black Mask. There, Black Mask executes police commissioner Loeb and then escapes while Batman confronts Black Mask's hired assassin Killer Croc. After defeating Croc, Batman learns that some of the world's deadliest assassins are in Gotham City to claim the $50 million bounty put on Batman's head by Black Mask. Batman tracks down the Penguin aboard his ship, believing he knows Black Mask's location. After arriving, Batman is forced to overcome the assassins Deathstroke and Electrocutioner, before learning from Penguin that Black Mask has been murdered in Lacey Towers. Batman travels to the towers and investigates the murder scene, piecing together that the victim was not Black Mask, and the murder may have involved a new criminal known as "the Joker".

Aiden is an Entity that has been linked to Jodie Holmes since birth. They are connected by an Ethereal Tether, that can be seen when switching to Aiden's view. This tether acts as a spiritual link between them that keeps Aiden bound to Jodie. Though he can travel farther away in some situations, the separation causes Jodie excessive amounts of pain and lasting disorientation. Jodie and Aiden seem to age in sync, for as Jodie grows older, Aiden grows stronger, and their bond grows greater. As the story progresses, it is revealed that Aiden is Jodie's stillborn twin brother. Jodie was delivered safely from her mother's womb, but her brother was strangled by the umbilical cord. Rather than passing on, his soul became linked to Jodie and remained that way, growing up as if it occupied a physical body.

Nine years after a failed robbery in the fictional town of Ludendorff, North Yankton, former bank robber Michael Townley and his family have relocated to Los Santos under a new identity. Michael is living a normal, but boring life, until he encounters Franklin Clinton, a gangster who seeks to elevate himself in the Los Santos underworld, and unexpectedly encounters Trevor Philips, the only other survivor of the bank robbery in Ludendorff. The three join forces to carry out a daring task to rob the Union Depository and seize tens of millions of dollars worth of gold. However, the trio find themselves being taken advantage of by corrupt Feds using the three to carry out their own agenda, as well as numerous confrontations with rival gangs and other criminals.