|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..."|
- For the similarly named prison, see Peña Duro.
- "For weeks, I've been waking up in strange places, not knowing how I got there or what I did. Driving myself mad! Thinking I had gone mad! And now I know that it was all your doing."
- —Edward Nygma to Oswald Cobblepot
A military task force, led by Eduardo Dorrance is called in to provide relief to Gotham. Meanwhile, Nygma looks for answers from Penguin, who leads him back to Hugo Strange. Then, Bruce is concerned about Selina's recent behavior.
Eduardo Dorrance, a soldier who once worked with Gordon, arrives in Gotham with the military. Nygma goes on the run after Gordon discovers that he blew up Haven, leading to a citywide manhunt. After regaining his memory of the same night the bridges blew, Nygma confronts Cobblepot and learns that Hugo Strange revived him. Strange reveals he implanted a chip in Nygma's brain to mind-control him; Gordon arrives and discovers Nygma's innocence. However, Dorrance reveals that he is the one controlling Nygma and activates the chip, forcing the latter to pursue Gordon. Simultaneously, Selina is declared a hero by the underworld for killing Jeremiah and turns away from Bruce, but Jeremiah awakens elsewhere, having fully recovered from his injuries.
- The Beat - Satan Takes A Holiday
- Dance On(You Fool) - The Mob
- Psycho - Grim Streaker
- "Pena Dura" is Spanish for "hard sentence."
- In the DC Comics, Peña Duro is a prison on the island of Santa Prisca and is best-known as the place where the supervillain Bane spent most of his life.
- In reality, "Peña Duro" is actually grammatically incorrect. Since "Peña" is feminine, the adjective should be the feminine "Dura", instead of the masculine "Duro".
- Interestingly, the Gotham episode named after the prison, "Pena Dura", uses the gramatically correct version. However, when the prison is later actually mentioned in the episode "Legend of the Dark Knight: 13 Stitches", Eduardo uses the incorrect name "Peña Duro", as it was called in the original comics. In the episode "Legend of the Dark Knight: I Am Bane", Eduardo mentions the prison once again. This time he calls it "Peña Dura", using the grammatically correct adjective.
- The arms trafficker Gerry Grekov is seen watching the 1953 thriller film Tangier Incident.
- One of the names on the arm's dealer's ledger seems to resemble the name Ben Edlund. Edlund was an executive producer and writer for Gotham, who wrote for some of the show's episodes.
- While Harvey is still talking to him at the GCPD, Bruce manages to stealthily sneak away and leave without Bullock hearing or seeing him do so. This is an allusion to the comics, in which Batman often manages to sneak away when other people are still talking to him without the other person even noticing it right away. Bruce previously did something similar during a conversation with Jim Gordon in the episode "A Dark Knight: Pax Penguina".
- As confirmed by Gotham writer Tze Chun, the coat worn by Bruce Wayne in "Pena Dura" and various other Season 5 episodes is a reference to the 1987 comic book story arc Batman: Year One by Frank Miller, in which Bruce Wayne was seen wearing a very similar coat.
- In the scene in which Nygma confronts Penguin at Gotham City Hall, it can be seen that Oswald stores two of his iconic umbrellas in a stand located right next to the door. Even though umbrella symbols were often used as Oswald's logo and trademark during Seasons 3 and 4, this marked the first time one of his actual umbrellas appeared since the episode "Wrath of the Villains: Unleashed".
- This was the last episode in which Butch Gilzean is mentioned.
- Jeremiah appears alive after seemingly dying in the previous episode. This is similar to the original comics and the animated adaptions of the Batman mythos, in which the Joker is known for his incredible ability to cheat death and survive deadly situations no matter the odds.
- Thomas Wayne's lair last appeared in Wrath of the Villains: Pinewood as well as the prequel novel Gotham: Dawn of Darkness.
- At the end of the episode, a surgeon unwraps the bandages off of two people that he transformed into Thomas and Martha Wayne doppelgangers. As soon as he sees the results of the operation, Jeremiah begins to chuckle maniacally. This appears to be a reference to a scene in the 1989 film Batman, in which Jack Nicholson's Joker went to the plastic surgeon Dr. Davis in order to have his face restored following the incident at Axis Chemicals. Once the surgeon takes off the bandages to reveal Joker's still disfigured, clown-like face and grin, Joker also begins to laugh maniacally.