|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"|
- "Our paths weren't meant to cross just yet. But I'm not going to kill you yet. I do that, you become the martyr, and she'll carry you in her heart forever. No, before I kill you, she has to hate you. And she will."
- —Mario Calvi to Jim Gordon
As the virus begins to spread in Gotham, the laboratory that is developing a cure is compromised. Mario and Gordon face off before the wedding, Selina meets an unexpected face and Barbara comes to Nygma with information about Isabella.
In Gotham Bio-Lab, a hematologist is working on finding a cure on Alice Tetch's blood. He goes to a bar, where Mario meets him. He is fearing that Gordon will continue waiting for Lee and asks the hematologist about the test on the virus. He refuses and Mario kills him in an alley, crushing his skull.
Bruce and Alfred are told by Jacob that Volk and his enforcer are dead. Certain that the Court has eventually discovered that they broke the deal, they decide to team up with Jacob. The GCPD is investigating the hematologist's murder, a man named Ryan Pfeffer and because of the smashed skull, Gordon suspects that Barnes may be responsible as the wallet reveals his position in the bio-lab. Barbara shows up at Dahl Manor and tells Nygma that Cobblepot is responsible for Isabella's death because he is in love with him but Nygma shrugs it off.
Jacob takes Bruce, Alfred and Selina to a building that the Court possesses. The building is guarded with two alarms in the roof and the basement. Bruce tells Selina that they will break in that day. At Gotham Bio-Lab, Gordon visits the facility in case someone uses Pfeffer's card but the guard tells him that the card was just used a few minutes ago. Gordon rushes to the lab and finds a doctor dead. Mario appears, attacks him and leaves him unconscious, but decides not to kill him. While Bullock tends him, they are told by Fox that the files were missing and Gordon's hand has "Arkham" written on it. He visits Arkham to question Tetch, deducing that he infected people before he was incarcerated and needs a name. Tetch refuses but accidentally reveals that the one he loves will die by hate and that he went from "healer to killer". Gordon instantly deduces that the killer is Mario.
Gordon has Mario tested but Fox states he's cleared of the virus. Gordon arrives at Lee's address and finds Mario and he deduces that Tetch injected him while he was experiencing the drug effects. Mario has Zsasz watch Gordon in the apartment but after a time, Zsasz lets him go. Nygma announces to Cobblepot that he plans on resigning and that they could continue working as partners but Cobblepot reveals his romantic feelings, giving Nygma the realization that Cobblepot indeed killed Isabella. He even contemplates killing him on a public awarding but can't make himself do it. Cobblepot wants things to go the way they were and Nygma seemingly agrees.
Gordon arrives at the wedding ceremony and finds Lee, in her dress, and tries to dissuade her from marrying. He subsequently realizes that Mario beat the virus through a cure in the files, had himself tested and told Zsasz to free him so he could arrive at the wedding and look like a jealous ex. Lee suggests that he gets help, causing Gordon to confess that he still loves her and that he did find her after his release, but backed off when he saw Lee happy with Mario. This causes Lee to cry and slap Gordon in the face and has Falcone take him out of the church. Gordon fails to beat them and Lee and Mario marry.
Lucius and Bullock discover that Mario's test came back off the charts and set out to find him. With Jacob and the gang dead, Bruce, Alfred and Selina enter the building to find the device. Selina is forced to walk on a wire to avoid alarms and opens the vault to find an owl sculpture. Talon arrives and attacks them, brutally wounding Alfred. A mysterious woman who has been following them arrives and distracts Talon and Alfred stabs a dagger in his neck, killing him. The woman reveals herself to be Maria, Selina's mom and they flee.
Nygma arrives at Sirens and decides to team up with Barbara, Tabitha and Butch to destroy Cobblepot and everything he loves. Lee and Mario arrive at a refuge in the woods before they leave Gotham. Gordon arrives with Falcone, demanding to know where he is. Falcone reveals that he knew something was wrong with Mario but that he didn't know about the virus. He eventually gives Gordon the location but makes him swear that he will bring him alive. Mario, now fully infected by the virus and certain that Lee still loves Gordon, is about to stab her when Gordon arrives and fatally guns down Mario, causing the knife to fall in the river. Lee looks at Gordon with shock and horror.