In the first season, a new recruit in the Gotham City Police Department named James Gordon is paired with veteran detective Harvey Bullock to solve one of Gotham City's highest-profile cases: the murders of Thomas and Martha Wayne. During his investigation, Gordon meets the Waynes' son Bruce who is now in the care of his butler Alfred Pennyworth. Meeting the younger Wayne further compels Gordon to catch the mysterious killer. Along the way, Gordon becomes involved with Gotham's Mafia families and associates including gangster Fish Mooney, Don Carmine Falcone, and Don Salvatore Maroni. Eventually, Gordon is forced to form an unlikely friendship with Bruce, one that will help shape the boy's future in becoming Batman.

       In the second season, Gordon deals with a series of events that are being secretly orchestrated by Theo Galavan and his sister Tabitha as part of an elaborate plan to take over Gotham and exact revenge against the Wayne Family with help from the Order of St. Dumas. After Galavan is subsequently murdered in his run for mayor, the enigmatic Hugo Strange and his assistant Ethel Peabody conduct a series of bizarre experiments underneath Arkham Asylum in the underground Indian Hill facility that is secretly owned by Wayne Enterprises and overseen by the Court.

       In the third season taking place six months later, Gordon has become a bounty hunter as he works to track down Indian Hill experiments that escaped six months earlier as well as a revived Fish Mooney who has recruited some of the Indian Hill experiments to form another version of her gang. While planning to get Leslie Thompkins back, he also encounters Carmine Falcone's son Mario Falcone. Gordon also has to tangle with hypnotist Jervis Tetch who arrives in Gotham City to look for his lost sister Alice.