|01 "Mad City: Better to Reign in Hell..."||09 "Mad City: The Executioner"||17 "Heroes Rise: The Primal Riddle"|
|02 "Mad City: Burn the Witch..."||10 "Mad City: Time Bomb"||18 "Heroes Rise: Light The Wick"|
|03 "Mad City: Look Into My Eyes"||11 "Mad City: Beware the Green-Eyed Monster"||19 "Heroes Rise: All Will Be Judged"|
|04 "Mad City: New Day Rising"||12 "Mad City: Ghosts"||20 "Heroes Rise: Pretty Hate Machine"|
|05 "Mad City: Anything for You"||13 "Mad City: Smile Like You Mean It"||21 "Heroes Rise: Destiny Calling"|
|06 "Mad City: Follow the White Rabbit"||14 "Mad City: The Gentle Art of Making Enemies"||22 "Heroes Rise: Heavydirtysoul"|
|07 "Mad City: Red Queen"||15 "Heroes Rise: How the Riddler Got His Name"|
|08 "Mad City: Blood Rush"||16 "Heroes Rise: These Delicate and Dark Obsessions"|
- "Jim, I knew if I saw you I might not have the courage to leave. And I need to. I finally understand Gotham in a way I suspect you always have. It's a place where the strongest and most cunning rule. Where the cost of survival is paid for by others, and everyone feels alone. Having the virus showed me the city as it truly was. As I truly was. In so many ways, the virus made me feel reborn. But if having the virus allowed Gotham to embrace its worst self, the cure should remind us there is always hope. A chance to remember who we can be, rather than who we are. I don't know if Gotham deserves saving, but I do know one thing, if anyone can save it, it's you. And in return, I believe it can save you as well. And then maybe one day, it will send you back to me. Until then. Love always. Lee."
- —Leslie Thompkins in her goodbye letter for Jim Gordon[src]
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.
Bruce withdraws the sword from Alfred's chest, spurning Ra's crowning as his heir. Ra's indicates Bruce to use the Lazarus Pit to heal Alfred and leaves. Bruce takes water from the Pit and pours it on Alfred's wound, waking him up. He then takes him to the hospital. Selina arrives later on, having heard about Alfred's condition, but is dismissed by Bruce for her flippancy. She counters that her actions have been based on what she considers surviving in Gotham, and that unlike Bruce, she's accepted who she is.
In the GCPD, Gordon receives a call from Lee, who is planning on leaving Gotham and wants him to join her. Gordon decides to leave with her in order to stay together. Nygma and Barbara begin to send demands to the mayor's office in exchange for the antidote, demanding Cobblepot in return. Gordon and Bullock then take Cobblepot out of his cell in order to bargain with them but Nygma has taken Tetch , planning on killing Cobblepot once and for all.
Gordon and Bullock take Cobblepot to a factory where Nygma holds Tetch with a hand grenade chained around his neck in order to kill him if the deal goes awry. The meeting is interrupted by Barbara , Tabitha and Butch who try to retrieve Tetch. Cobblepot breaks free, knocks out Nygma and escapes in the police cruiser with him in the backseat. Seeing they cannot escape in time, Gordon cuts Tetch's throat to retrieve his blood for the antidote and he and Bullock return to the GCPD to develop the cure. Unfortunately, Gordon finally succumbs to the virus and leaves the precinct. He tries to inject Lee with the antidote but he fails multiple times. While he and Lee escape through the train station, Bullock intercepts them but Gordon attacks him while Lee boards the train. Harvey urges him to remember his calling, and affirms his friendship with Jim before giving him his badge back with another vial of the antidote on the back. In the train, Gordon injects himself and Lee, freeing them from the virus.
Barbara confronts Butch about the betrayal and shoots him in the center of the forehead. She then confronts Tabitha in one of their safe houses and ends up fighting, culminating in Tabitha using her whip to cause an electrocution, killing Barbara.
Nygma breaks free of Cobblepot's handcuffs and apparently goads him into returning to the port where he shot Cobblepot. However, this is part of Cobblepot's plan, having emptied Nygma's gun and reveals that Ivy and Fries followed them in order to complete his task: to contain Nygma as a reminder to never let love weaken him again. Cobblepot then has Fries freeze Nygma as he comes after him in indignant fury. Alfred finally wakes up from the coma and comforts Bruce, urging him to forge his destiny based on what he loves.
Wanting to find security and influence, Selina goes to The Sirens and gains mentorship under Tabitha, even testing her whip. Gordon receives a letter from Lee, stating that she is leaving Gotham but that she believes in him. Cobblepot and Ivy display Nygma's frozen body as a new sculpture for their new club: the Iceberg Lounge. Butch's body is revealed to be on life support in the hospital and the doctors find that his birth name was changed from Cyrus Gold. In the final scene, a family wanders through the streets when they are assaulted by a mugger. Suddenly, a vigilante is shown attacking the mugger and escaping to a building rooftop. The vigilante is revealed to be Bruce. He then stares into the city as a storm is heard in the background.
- Butch is revealed to actually be comic canon supervillain Cyrus Gold, a.k.a. Solomon Grundy.
- Additionally, Butch is revealed to be 35 years old.
- The title references the twenty one pilots' song of the same name.
- This is one of two season finales starring Jessica Lucas (Tabitha Galavan), the other being "A Dark Knight: No Man's Land".
- The final episode was to be broadcasted on a Monday, as the series was later rescheduled to air on a Thursday as of the fourth season.