Some of Gotham's most unhinged villains band together, while The Riddler continues his conquest of the city. Gordon is on a search for answers and all roads keep leading him back to the Court of Owls. Meanwhile, as Alfred begins to notice a change in Bruce, Bruce 2 confides in Selina.

Gordon tracks down the weapon the Court of Owls intend to use for the destruction of Gotham; Kathryn and Temple Shaman tell Bruce about their next move; Ivy offers Selina help.

With the deadly virus spreading throughout the city, the search for the antidote continues, as Fish Mooney, The Riddler and Penguin reveal plans of their own. Bruce meets Ra's al Ghul and completes his last task in order to fulfill his destiny, but realizes he can't let go of his past. Meanwhile, Gordon tries to win back Lee, and past alliances within Gotham City are broken, while new alliances are formed.