|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..."|
- "Alexander the Great looked upon his land, and wept, for there was nothing left to conquer. I've done all I can in Gotham, sometimes twice. There's nothing left for me here."
- —Oswald Cobblepot to Selina Kyle[src]
Gordon assembles an unlikely team to protect Gotham from Eduardo Dorrance and his Delta Force. Just as Lee Thompkins resurfaces, Barbara reveals shocking news that will change Gordon's life forever. Meanwhile, Selina and Penguin team up to outsmart fellow villain Magpie.
Gordon destroys the chip in Nygma's brain, and Lucius surgically removes it. Dorrance and his men take control of the GCPD; Gordon, Bruce, Alfred, Lucius, Nygma and Barbara work together to broadcast evidence of Dorrance's criminal activities to the press and retake control of the GCPD. Simultaneously, Gordon and Dorrance face off after the latter reveals he has Lee in his custody and that Haven was destroyed to ensure that the military would maintain that the city was beyond saving. Gordon impales Dorrance with a pipe and takes Lee to the GCPD, but Dorrance's superior, Theresa Walker, takes him to Hugo Strange and activates a second chip in Lee's brain, which Gordon manages to destroy as well. Meanwhile, Cobblepot and Selina make a deal to escape from Gotham by working together to track down and kill a thief named Magpie after she steals from the former. Soon after, Alfred is kidnapped by Jeremiah, and Barbara reveals she is pregnant with Gordon's child.
- Originally titled "The Air is Getting Slippery", "13 Stitiches" was named after the NOFX EP of the same name.
- The villain Magpie appears in her first live-action appearance. She appears as a thief obsessed with shiny things, who steals from Penguin.
- However, there is no mentioning of her true identity of Margaret Pye.
- The villain Bird, Bane's right-hand man in the comics, makes his live action debut. Although his real name is unknown in the comics, "Angel Vallelunga" is borrowed from the video game Batman: Arkham Origins.
- Lee Thompkins last appeared in "A Dark Knight: No Man's Land".
- Barbara Kean is revealed to be pregnant with James Gordon's child, alluding to some of their offspring from other DC media, most especially Barbara Gordon and her siblings James Gordon Jr. and Tony Gordon (although Tony's mother is established to be Thelma Gordon even though he is still the full biological brother of his universe's version of Barbara Gordon).
- Lucius Fox and Bruce Wayne being manipulated by a female villain to use the Wayne reactor cores as a way of killing the citizens of Gotham have very similar parallels to their roles in the film The Dark Knight Rises.
- This is the most amount of time where Selina Kyle and Oswald Cobblepot are in a scene(s) interacting.