In the wake of Mario's death, a vengeful Falcone sends Zsasz to kill Gordon; however, after seeing what the virus has done to Barnes, Lee realizes Gordon may have been justified and persuades Falcone to call off the hit. Unhinged by ghostly sightings of his father, Cobblepot insults Gotham's citizens on live TV and murders his Deputy Chief of Staff, unaware that Nygma is orchestrating his downward spiral. Selina accepts her mother Maria (Ivana Milicevic) back into her life, but later learns Maria owes money to criminal Cole Clemons. Investigating the discovery of a briefly reanimated corpse, Gordon and Bullock pursue ex-Indian Hill employee Dwight Pollard (David Dastmalchian) as he prepares to resurrect another corpse: Jerome Valeska.

Infected by Alice Tetch's blood, Mario vows to make Thompkins hate Gordon. To do so, he orchestrates a series of events that make it appear to her that Gordon is trying to sabotage their marriage. The plan works, and just before Mario and Thompkins' wedding, Thompkins vows never to see Gordon again. On their honeymoon, a deranged Mario attempts to kill Thompkins, but Gordon arrives and guns him down, much to Thompkins' shock. Barbara informs Nygma that Cobblepot killed Isabella because he's in love with him. After verifying this information, Barbara and Nygma plan to betray Cobblepot and usurp his power in the mob. When Bruce and Selina attempt to use their key to break into a vault, they are intercepted by Talon. With the help of Alfred, they kill Talon as Selina's mother reveals herself to them and helps them escape.

Bruce learns the gang who’s after the key is out to destroy the Court of Owls and is therefore not his enemy. Soon after, Talon murders the gang leader. When Mario is targeted by assassins, Falcone deduces that the Court is responsible and successfully blackmails them into ceasing their attack. Nygma kidnaps and tortures Butch and Tabitha, before discovering that they are not responsible for Isabella’s death. Showing remorse after cutting off Tabitha’s hand, he allows them to go the hospital. After investigating the matter, Barbara realizes Cobblepot killed Isabella and plans to use the truth to turn Nygma against him. Gordon makes one final goodbye to Lee before her upcoming wedding day with Mario. When Mario sees Lee with Gordon from a distance, he lets out a fit of rage and shows symptoms of the Tetch virus.

Driven mad by the virus, Nathaniel Barnes has become a vigilante, murdering any criminals that cross his path. After Gordon becomes suspicious of Barnes, he attempts to frame Gordon for the murder of a low-level criminal, but is unable to convince the GCPD. After a showdown, Barnes is arrested and incarcerated in Arkham Asylum. After Cobblepot kills Isabella, Nygma suspects Butch Gilzean for the act. Cobblepot promises to help bring retribution to Butch. Ivy Pepper reveals herself to Bruce and Selina in her new adult form. However, she is followed by people seeking to kill her. The three of them escape, believing that they were being hunted because of a necklace that Ivy stole. They are convinced otherwise when they discover that the original owner of the necklace is dead and that the necklace contains a key.

After Gordon rejoins the GCPD, Barnes loses control and kills a criminal instead of arresting him. He later visits Jervis Tetch in Arkham Asylum, demanding to know if the virus can be cured, but Tetch says it's only a matter of time before it takes him over. Barnes begins hearing voices that urge him to kill more criminals. Lee and Mario have an engagement party, where Barnes makes plans to turn himself to police custody. However, his psychosis overcomes him when he learns Dr. Symon, a killer he arrested, has been released thanks to his powerful connections. Losing faith in Gotham's justice system, Barnes kills Symon and plans to murder criminals on a larger scale. 53 9 "The Executioner" John Behring

Vale recovers but ends her relationship with Gordon, knowing he manipulated Tetch into shooting her instead of Lee. Tetch breaks into the morgue and drains the blood from Alice's corpse. He also exposes Gordon to a powerful hallucinogen called the "Red Queen", causing intense hallucinations that bring Gordon to the GCPD, a life where he is married to Lee with two children, and an encounter with his deceased father who encourages him to be a better protector for Gotham. Mario finds and brings Gordon back to consciousness. Cobblepot attempts to manipulate Isabella and Nygma into breaking off their relationship, but to no avail. Barnes loses control and attacks a suspect while questioning him over the break-in; he and Bullock learn Tetch is planning to spread the virus at a founders' party, and arrest him in time. Gordon decides to honor his father by rejoining the GCPD.

Tetch sends a white-suited man (Kieran Mulcare) to lure Gordon to a ringing phone. Tetch tells Gordon he needs to choose between saving the married couple from jumping to their death, or saving a boy who would be run over by a hypnotized driver. Gordon chooses to save the boy, and watches in horror as the married couple fall to their deaths. He later receives another call from Tetch, telling him to meet at a new address. It is revealed that Tetch has kidnapped Valerie and Lee. After talking with Mario, Gordon breaks in at the address, but is forced to sit at the table for the tea party. After Tetch asks Gordon who he should kill Gordon says Lee, but Tetch shoots Valerie instead. Gordon and Lee rush Valerie to the hospital. Meanwhile, Cobblepot realizes that he's in love with Nygma and plans to confess his feelings to him, but Nygma meets a woman named Isabella, who reminds him of Kristen Kringle.

Cobblepot's term as mayor starts off well, but a new Red Hood Gang appears and openly challenges his authority. Nygma discovers that Butch is behind the new gang, as part of a scheme to make himself Cobblepot's right-hand man again. At a celebratory party in the mayor's honor, Nygma manipulates Butch into exposing himself as the mastermind behind the Red Hoods, thus reinforcing his own position as Cobblepot's most trusted friend and ally. Barnes asks Lee about the tests on Alice Tetch's blood, without revealing that he was exposed to it. At Gordon's suggestion, Bruce tells Selina how he feels about her, but she dismissively tells him that he only feels that way because he's never dated anyone. Bruce reasserts his feelings, and Selina kisses him. Elsewhere, Jervis Tetch mourns his sister's death and plots revenge against Gordon.

Five assists Selina in robbing a bar and rescues her when she is captured, but she sees the scars on his body and identifies him as an imposter. Five admits he wanted to experience a normal life by socializing with someone, but Selina reassures him that he is more normal than he thinks, and they kiss. Tetch hypnotizes the wrestling Tweedle Brothers to help him break into GCPD and kidnap Alice, but Gordon and Bullock track them down. Gordon finds himself still under the suicidal influence of Tetch's hypnosis; realizing his suicidal urges are connected to his issues with Lee, Gordon overcomes them and breaks the spell. Alice falls and is impaled on a pipe, leaving a grief-stricken Tetch to escape. While investigating the crime scene, Barnes becomes infected by Alice's dripping blood. Cobblepot bribes campaign officials to buy the election, but Nygma takes the money back; to Cobblepot's shock, he wins the election anyway, and realizes Nygma wanted to show him that the people genuinely want him as Mayor. Five bids farewell to Bruce and tries to leave Gotham, but is kidnapped by the Court.

Hypnotist Jervis Tetch (Benedict Samuel) hires Gordon to find his sister Alice (Naian Gonzalez Norvind), an Indian Hill escapee whose blood contains a virus. Barnes offers Lee her old job back at GCPD. Cobblepot runs for mayor to clean up Gotham's corrupt system; to aid with his campaign, he has Edward Nygma declared legally sane and released from Arkham. Gordon gets into a brawl and is stitched up by Lee's new fiancé, Mario Calvi (James Carpinello), at the ER. After Alice tells Gordon she wants nothing to do with her brother, Gordon questions Tetch, who hypnotizes him into nearly committing suicide. Alice saves Gordon, who brings her into GCPD. Lee and Mario have dinner with Mario's father, the ex-Don Carmine Falcone. Bruce takes in his doppelgänger—subject 514A, a.k.a. "Five"—who demonstrates impressive fighting skills and an imperviousness to pain. Five later impersonates Bruce and takes an oblivious Selina out on the town.