|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 chemical plant the episode is named after, see Ace Chemicals.
- "Why don't you understand? You need me! I'm the answer to your life's question! Without me, you're just a joke... without a punchline!"
- —Jeremiah Valeska to Bruce Wayne[src]
Gordon races to uncover the criminal element threatening to end talks of Gotham's reunification with the mainland. A very much alive Jeremiah returns and organizes a twisted recreation of the murder of Bruce's parents with the help of Jervis Tetch.
- The Mad Hatter last appeared in "A Dark Knight: That's Entertainment".
- This episode marks Benedict Samuel's final appearance as Mad Hatter on the show.
- This marks the first appearance of the Ace Chemicals plant since the season 2 episode "Wrath of the Villains: A Dead Man Feels No Cold".
- Although Martha and Thomas Wayne do not reappear in the flesh, they are impersonated by lookalikes played by the same respective actors from the pilot. This episode marks the first time that actors Grayson McCouch and Brette Taylor have filmed any new scenes since the first episode.
- The Wayne Manor study set has its final appearance on the show.
- The episode showcases the first onscreen appearance of the Monarch Theatre on the show. Prior to the episode, the theater appeared unnamed in the tie-in novel Gotham: Dawn of Darkness.
- The episode is the first to reveal the film Mark of Zorro as the film that Bruce and his parents watched on the night of the murder. Prior to this episode, tie-in materials for the series simply referenced it as a musical.
- It is revealed that Bruce's parents were killed on June 27.
- Jeremiah's plan to execute Leslie and Gordon in the alleyway could be a subtle homage to Jack Napier/The Joker being responsible for killing Thomas and Martha in the 1989 Batman movie. In similar fashion, the name of the theater was first established in the same film, later becoming a staple in future Batman media.
- Valeska's chemicals contaminating the Gotham River is a reference to Detective Comics #475 (February 1978), in which the Joker decides to poison Gotham's water system with his hideous Laughing Toxin, leading to the creation of the infamous Joker Fish.
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