Five years later, Jim with a role pivotal to the GCPD, Bruce becoming the "The Dark Knight", and villains becoming who they are. Jim has hands full at the GCPD with Zeus and the alliance of villains banding together to make trouble around the streets. Bruce finds out why his role is so important in Gotham and Arkham. Encountering Jeremiah, Alfred has a time with some laughing gas.
Bruce finds his ultimate goal to find Alfred, with that going on, Bruce finds Jim to help him out to find where Jeremiah keeps Alfred. Alongside, the "Band of Villains" try to be more difficult to catch with Jim's point of view. Harvey gives in to the darkness that he has. Jeremiah puts on a concert performance for everyone in Gotham to see what he thinks of Bruce, the Knight that Serves.
Arkham's finest give in Gotham. Jim finally has a villain in custody, with that, he tries to allocate where the others are and what they are planning. Meanwhile, Bruce comes to terms that he is not the Dark Knight in his eyes. In the short time, a new pivotal stance comes to Gotham with Ra's Al Ghul giving in with a "event" for Gotham.
Jervis Tetch, an escapee around Arkham Asylum, gives Gordon a "sign" of death nearby. Whilst, Jeremiah gives in to the GCPD about the breakout. Bruce is forced to put his limits to the test around Gotham and fights crime all-time high.
With Jeremiah giving the GCPD a scare, Jim Gordon decides to give into what Jeremiah said prior to they're last confrontation, Meanwhile Penguin has an army built for Jeremiah and the city has gone havoc around chaos. Bruce is force to deal with Jeremiah and his planned attacks against Bruce. Jervis brainwashes half of the entire population of Gotham and Arkham. Then, Jim is forced to play with Jervis's friend, the Caterpillar.
Jim Gordon teams up with one of his military friends, Floyd Lawton. Meanwhile, Jim Gordon works with the army to help regain the city back from Jeremiah. Later, Jeremiah finds the real "Joker" from his brother's cult followings. Lastly, Floyd gets a taste of being a "metahuman" from Professor Hugo Strange.
In attempt to get Floyd, Jim tries to find Hugo Strange knowing he knows where Floyd is. Harvey tries to crack a case on child snatchers around Gotham. Meanwhile, Jeremiah knows all about the "Joker" persona and what's to learn about the first one ever produced in Arkham. Lastly, Floyd becomes Deadshot tricking Jim that he's one of the "good ones".
With Floyd lying low, Clayface makes a gratuitous comeback, only this time he's got an army. With allying with Jeremiah and The Joker, Clayface decides to pick Jim Gordon as a pivotal target and invites him to the "Monarch Theater" for a big surprise. Meanwhile, Harvey deals with Scarecrow as a complete diversion to Jeremiah's plan. Lastly, Penguin unleashes a little madness against the city with a "clever" friend in contact.
Penguin has gone awry with the city regaining insanity and wants a piece of the city from the GCPD. Meanwhile, Jeremiah has been put in confinement after the events of the show. Then, Jim Gordon has ran into an old friend of his, Morris Tetch.
Jim Gordon builds an unlikely alliance with Nygma to stop Penguin from any rash harm to the city. Meanwhile, Morris Tetch is on a mission to find his invalid sister only to find out she runs a clock shop. Soon after, Bruce confronts Penguin in an unlikely matter.
In a previous matter, Morris Tetch had a mission to find his invalid sister, now he's bringing havoc upon the city of Arkham. Meanwhile, Penguin is placed in confrontational confession for his wrong doings. Soon after, Bruce finds the real reason about his parents murder. Then, Jim Gordon has to stop the villain known as, "The Clock King".
Bruce retains information about how his parents were killed and who killed them. Meanwhile, The Clock King has something planned for the city and Jim Gordon is force to deal with those inner thoughts. Soon after, Alfred tries to stop Bruce, in the race for the clock, to stop Bruce from finding who killed his parents.
The Clock King, in motion-ransom, has his sister held captive against her will. Meanwhile, Jim Gordon tries to find the missing sister in connection with the Clock King. Soon after, Bruce is very unhappy about who killed his parents. Later, Selina and Bruce form a team to take down who killed his parents, to finally end this life-changing destruction.
In escaping the city as a plan, the Clock King is trying to blow up the bridges knowing thousands of people will die and suffer mid-through. Meanwhile, Jim Gordon fights with inner demons to only try to stop the Clock King. Soon after, one clever villain decides to help the Clock King in wrong doing's, helping his create havoc and chaos around the city, all-time high.