|01 "Year Zero"||07 "Ace Chemicals"|
|02 "Trespassers"||08 "Nothing's Shocking"|
|03 "Penguin, Our Hero"||09 "The Trial of Jim Gordon"|
|04 "Ruin"||10 "I Am Bane"|
|05 "Pena Dura"||11 "They Did What?"|
|06 "13 Stitches"||12 "The Beginning..."|
- "This city will never be what you want it to be, Jim. It's always going to belong to the bad guys, like me."
- —Victor Zsasz to Jim Gordon
Gordon and Penguin are forced to work together and alliances are shaken when Lucius, Nygma and Barbara all have different ideas of the culprit behind recent events at Haven. Meanwhile, Selina continues her quest for revenge against Jeremiah.
Day 96: Following the destruction of the haven, Gordon and Cobblepot reluctantly work together to track down Victor Zsasz, who is suspected of being the perpetrator, though he protests his innocence. After capturing him, Gordon asks Lucius to find evidence on Zsasz's guilt, and the latter encounters the disillusioned Nygma, who has discovered numbers written onto his hand from the previous night. Lucius and Nygma reluctantly work together to find the evidence and this proves Zsasz's innocence. However, Nygma learns that the numbers are for the apartment of a witness who saw him do the deed; after regaining his memory of the event, Nygma kills the witness. Cobblepot captures Zsasz and organizes a kangaroo court in which the survivors of the event ignore the evidence and order Zsasz's death, though Gordon and Bullock rescue him and they let him go free, inadvertently turning the remaining refugees against them; after drowning his sorrows, a drunken Gordon reunites with Barbara and they kiss. Meanwhile, Bruce and Alfred track down Selina, who follows Ecco to Jeremiah, and she manages to stab him repeatedly before being rescued by Bruce and Alfred.
- This episode literally takes place right after the events of "Legend of the Dark Knight: Penguin, Our Hero", picking up mere seconds after the destruction of Haven at the end of the last episode. This is the only instance on the show where this is the case.
- Some of Penguin's old election posters that encourage citizens to vote for Cobblepot reappear. They can be seen in the Upper East Side territory of Victor Zsasz. These posters were last seen when Penguin ran for mayor during Season 3.
- This episode would have featured the final appearance of Anthony Carrigan as Victor Zsasz, however after FOX granted Gotham two additional episodes for the fifth season, this allowed Carrigan to reprise the role for the final time in "Legend of the Dark Knight: The Trial of Jim Gordon".
- Jeremiah Valeska's hat highly resembles one of the hats Joker was seen wearing in the 1988 graphic novel Batman: The Killing Joke.
- The scene in which Jeremiah and Ecco dance at the Soothsayers' lair is a reference to the iconic cover of the 1999 one-shot comic Batman: Harley Quinn, which pictured the Joker and Harley Quinn in a similar dancing pose. Batman: Harley Quinn marked the first appearance of Harley Quinn in main DC comics continuity. Like the Gotham episode Ruin, the one-shot comic took place during the No Man's Land crisis. The cover of this comic was previously also alluded to in the 2016 DCEU film Suicide Squad.
- Victor Zsasz alludes to the comic book origin of his character when he states that his body would be covered in tally marks had he truly been the one to kill the people in the building. His scars were last seen in Penguin's Umbrella.
- Nygma's killing of the old woman in the apartment highly resembles his counterpart's first kill in the movie Batman Forever. In that movie, that version of Nygma pushed his ex-boss Fred Stickley on a computer chair towards the edge of a window. Nygma then fooled his boss into thinking he was about to save him, when really Nygma was going to finish pushing him out the window while telling him that he is fired. In similar fashion, Nygma in the episode momentarily pretends to have mercy on the old woman's predicament, but then proceeds to wheel her to her death through the window.
- Prior to that scene, Nygma also uses the phrase "deaf as a bat", which is simlar to a famous line uttered by Jim Carrey's version of Nygma in Batman Forever.
- During Zsasz' tribunal, Penguin is trying to use a guillotine to execute Victor. When asked by a fan where Cobblepot got the vintage guillotine from, writer James Stoteraux answered that "it was raided from the Gotham Museum of Antiquities". In fact, it later turns out in "Pena Dura" that Cobblepot stole almost everything valuable in Gotham City and had his men raid and loot dozens of buildings and museums, which would match the backstory for the guillotine.