Season 5

Complete listed story — includes the ending

1. Year Zero

Due to the bridges being bombed, the government has declared Gotham off-limits from the mainland, allowing criminals to control entire boroughs and neighborhoods. Gordon and the remaining GCPD officers gather refugees into the precinct for safety, while Bruce and Gordon work together to rid the city of crime. Scarecrow and his followers steal most of the GCPD's food and medicine, forcing Bruce to have Wayne Enterprises illegally fly supplies into the city. Cobblepot unsuccessfully tries to steal the supplies, and the resulting gunfight leads to Tabitha's death. Meanwhile, Nygma suffers memory blackouts and wakes up in different locations. Selina undergoes surgery to prevent her spine from collapsing, but remains paralyzed. When Selina unsuccessfully attempts suicide, one of the hospital's nurses advises Bruce to seek out "The Witch" to save her life.

2. Trespassers

Bruce hunts down the Witch and discovers her to be Ivy, who has been captured by locals after killing instead of helping them. Ivy's powers have grown and allowed her to control plant life, which she feeds the corpses of anyone who enters her territory – the park. Despite this, Bruce convinces her to save Selina and reluctantly frees her in the process; she gives Bruce a seed that will repair Selina's spine but will also "change" her forever. Selina ingests the seed and regains the ability to walk, but also gains cat-like qualities. Gordon and Bullock discover a runaway child who claims to have been a slave for an outlaw gang. Gordon and Bullock rescue the children and bring them to the "Haven" safe zone, with Barbara saving Gordon in the process after Cobblepot places a bounty on him. Meanwhile, Nygma awakens and realizes he has kidnapped a gangster working for the Street Demons, though they have seemingly been killed by Cobblepot.

3. Penguin, Our Hero

After her recovery, Selina escapes from the hospital and she and Bruce work together to track Jeremiah Valeska down to the dark zone of the city, where they discover that Ecco is recruiting people to work for him. Selina fakes wanting to work for Jeremiah to break into their headquarters, but after a showdown, Ecco escapes and Selina betrays Bruce to go after Jeremiah. Meanwhile, Cobblepot's men defect to Haven and he leads a small army to the area, where he captures Gordon and the refugees. However, the Street Demons, believing Cobblepot killed their men, take him prisoner and kill the defected thugs, forcing him and Gordon to work together and free themselves before killing the Street Demons. However, as Gordon allows Cobblepot to go free, Haven is blown up by an unknown perpetrator, killing the refugees.

4. Ruin

Following the destruction of 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 of Zsasz's guilt, and the latter encounters the disillusioned Nygma, who has discovered numbers written on his hand from the previous night. Nygma helps Lucius find the evidence, which proves Zsasz's innocence. Afterward, Nygma learns the numbers are for the apartment of a witness who saw him blow up Haven; regaining his memory of the event, Nygma kills the witness. Cobblepot captures Zsasz and organizes a kangaroo court where the Haven survivors ignore the evidence and order Zsasz's death, though Gordon and Bullock rescue him and 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, Selina follows Ecco to Jeremiah and manages to stab him multiple times, before being rescued by Bruce and Alfred.

5. Pena Dura

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.

6. 13 Stitches

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 the 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.

7. Ace Chemicals

On the anniversary of the Wayne murders, Jeremiah uses two surgical doppelgangers of Thomas and Martha Wayne to force Bruce to relive his parents' deaths, hoping to become "connected" to him. Bruce and Alfred escape as Jeremiah blows up Wayne Manor, and Selina abandons Cobblepot to assist Bruce. Gordon and Lee discover Jeremiah is developing a toxin at Ace Chemicals, and are hypnotized by the Mad Hatter. Jeremiah kills the doppelganger couple and attempts to execute Gordon and Lee at Crime Alley, but Bruce and Selina rescue them. Jeremiah activates the toxin, forcing Gordon to drive it into the Gotham River; due to the water pollution, the government decides against mainland reunification. After a showdown with Bruce at Ace Chemicals, Jeremiah falls into a chemical vat and is left disfigured and brain-dead. Barbara, for the sake of her unborn child, forms a truce with Cobblepot and Nygma, who plan to escape Gotham on a self-built submarine.

8. Nothing's Shocking

As Cobblepot and Nygma work on building the submarine, they are approached by Cobblepot's accountant Arthur Penn, who survived his near-death experience at Haven. However, Penn suffers from a split personality, embodied by the ventriloquist dummy Scarface, leading to a confrontation that results in Penn's death. Bruce and Alfred track down a missing man in the sewers and rescue him from a hybrid-human who was mutated by Jeremiah's chemicals. When two former GCPD officers are murdered by shapeshifting Indian Hill escapee Jane Cartwright, a.k.a. " Jane Doe ", Gordon discovers she is linked to Bullock's early years at the GCPD with Dix, his old partner. After Jane kills Dix, Bullock tracks her down and is forced to kill her. A guilt-ridden Bullock then confesses that he and the victims unethically forced Jane to incriminate her mother for killing her abusive father, and Gordon tells him he cannot offer forgiveness.

9. The Trial of Jim Gordon

Gordon tries to negotiate a ceasefire between Gotham's gangs but is shot by Zsasz and left comatose. As Lee operates on him, Gordon dreams of himself being on trial for his failures in his life and decisions. Bullock discovers Zsasz was acting under Ivy's influence, as she intends to prevent reunification and rebuild Gotham with her plants. Ivy also hypnotizes Bruce and Lucius into shutting down the river's treatment facility and keeping the water polluted, but Selina frees them and helps stop the shutdown. To get in Gordon's good graces, Barbara blackmails the gang leaders into a ceasefire. Ivy infiltrates the GCPD to kill Gordon but flees after Lee shoots her. In his final hallucination, Gordon decides to live for Lee and his unborn child. A month later, Gordon and Lee are wed by Bullock in the precinct, while Bruce shares a passionate kiss with Selina; disappointed, Barbara hopes to escape Gotham soon alongside Cobblepot and Nygma and keep the baby for herself.

10. I Am Bane

The government approves mainland reunification and sends the military to commence the procedure. However, Dorrance—transformed by the strength-enhancing drug "Venom" and now calling himself Bane —captures Gordon, Bruce, and General Wade. Walker reveals herself as Nyssa al Ghul, the daughter of Ra's al Ghul, and tortures Gordon in front of Bruce as punishment for killing her father. Bane is sent to kill Barbara, who undergoes labor at Lee's clinic. Cobblepot and Nygma are prevented from escaping after Barbara steals the submarine's pressure gauge, forcing them to protect her from Bane before stealing back the gauge. Alfred and Selina fight Bane, who defeats them and badly injures Alfred. As Barbara gives birth to her daughter, Lee convinces her that she does not have to leave Gotham and they can work out raising the baby. However, they are captured by Nyssa. Bruce frees himself and rescues Gordon and Wade, but the latter, now controlled by Strange, orders the military to bomb Gotham.

11. They Did What?

Following the city's bombing, refugees retreat to the GCPD while Bane takes command of the military. Cobblepot and Nygma decide to remain in Gotham and stand with the GCPD against Bane's forces. Selina retrieves Lee, and she and Bruce use one of Jeremiah's recommissioned bombs to destroy Wayne Enterprises' headquarters, slowing the military's advance. Gordon rescues Barbara and the baby from Nyssa, who kills General Wade and escapes Gotham by stealing the submarine. In a final standoff with the GCPD and the refugees, the military turns on Bane, who surrenders. Gotham's reconstruction begins, and Gordon is appointed Commissioner of the GCPD. Realizing she did not give her baby a name throughout the chaos, Barbara decides to name her daughter Barbara Lee Gordon, after the three people she trusts. Elsewhere, Cobblepot and Nygma plan to eventually take over Gotham, and Bruce departs from the city, promising to return.

12. The Beginning...

Ten years later, Bruce returns to Gotham following his extensive travels across the world and his reappearance is publicly announced. Cobblepot is released from Blackgate after a decade in custody, and Gordon wants to retire from the GCPD, though he relents when Nygma, who has been incarcerated at Arkham Asylum for a decade, escapes and kidnaps Mayor James to destroy Wayne Tower at its reopening. However, Nygma is a patsy as they successfully defuse the real bomb. Simultaneously, Cobblepot frees Nygma once again while Bullock frames himself for the murder of the guard who broke Nygma out from prison, though Gordon frees him after learning that Jeremiah Valeska, who has faked brain death, is the true culprit. Bruce, now secretly working as a vigilante in a bat-themed costume, captures Cobblepot and Nygma; after they break out of a prison van, they decide to seek revenge on the vigilante but remain afraid of him. Jeremiah kidnaps Barbara Lee in a showdown with Gordon, though she is rescued by Bruce. Finally, Bruce reconciles with Selina, who has become a cat-themed burglar, and is summoned by Gordon using a police searchlight bearing a bat emblem.