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.

Bruce is brought before the leader of the Court, a woman named Kathryn, whom he recognizes from various Wayne functions. He is ordered to cease his investigations into them, Wayne Enterprises, Indian Hill, and the deaths of his parents, to which he obliges in exchange for the lives of those closest to him. Ivy washes ashore as a grown woman. Fish captures Bullock and uses her powers to make him lead her to the secret facility holding Strange. Gordon makes a deal with Fish to help her escape with Strange if she hands over Harvey. Gordon informs Penguin of her escape route. Penguin prepares to kill her but, when she reveals that she let him live because he was her greatest creation, he lets her go. The mob breaks into the facility and kills some of Fish's monsters. Valerie visits Gordon about his deal with Fish and they share a kiss. Bruce's doppelgänger breaks into Wayne Manor. Meanwhile, Lee returns to Gotham.

Six months after the last sighting of Fish Mooney, Lee has moved on and has a new man in her life while Gordon becomes a bounty hunter to track down the Arkham Asylum escapees. Penguin puts a $1,000,000 bounty on Fish, dead or alive. He visits Nygma and feels that Fish has an ulterior motive. Gordon, with the help of enthusiastic reporter Valerie Vale (Jamie Chung), tracks down Strange's assistant Ethel Peabody but she is captured and killed by Fish. A suspicious Ivy spies on them and is caught. Fish orders her killed, ignoring Selina's protests, but she runs and falls down a sewage pipe but not before being touched by one of Fish's monsters, the one who can drain the youth out of a person. Bruce and Alfred return to Gotham and in a meeting with the Board of Directors, Bruce threatens to expose their wrongdoings unless he gets a face-to-face talk with the person who was in charge of Strange. The Court sends Talon to Wayne Manor and he kidnaps Bruce. Meanwhile, the mysterious doppleganger Bruce Wayne is lurking around Gotham City.

While Gordon, Bruce and Lucius remain at Indian Hill, the city of GOTHAM will be met with a new threat as Hugo Strange’s inmates devise a plan to escape and start their new lives in GOTHAM

Selina is chased by Bridgit around the test room and she unsuccessfully hits Bridgit unconscious and steals her weapon. This proves unusable as Bridgit awakens and the flames are easily absorbed by her suit. Selina then begs to be Bridgit's servant, making use of Bridgit's alter-ego. Bruce is troubled after Selina fails to meet with him and understands of her capture. He alerts Gordon, Alfred, and Lucius Fox, who plan to break her out. Meanwhile, Hugo Strange's project continues and he successfully resurrects Fish Mooney - the first subject to retain full memory. She discovers that she has powers of controlling people by touching them after an encounter with an Arkham worker. After a discussion with Lucius Fox, Bruce is told that there is likely a secret room in Arkham where Strange is experimenting on the dead, and the only way to be certain is if they head in themselves. Bruce and Fox visit Arkham executing their plan to distract Strange as well as find the entrance to the room in the process and smuggle Gordon in to look, however their motives are revealed and all three are captured. Bruce and Fox are put in a chamber and are interrogated by Nygma on Strange's behalf, who demands that they reveal their knowledge or face lethal gas released by nozzles in the ceiling. Meanwhile, Gordon is brought into another room with Strange, who replicates him into anotherinmate, which proves successful.

Together with Bullock and a crew of police officers, Gordon arrives at Arkham Asylum with a warrant to inspect Professor Strange's office. Strange is unfortunately one step in front of them, having shredded all of his documents. Nygma in the meantime, is disturbed at Indian Hill, and realizes he needs to escape. As Captain Barnes is still in the hospital, Harvey Bullock is declared de facto captain. Bruce decides to go of with Selina to find a way in to Arkham. Selina accepts it, and thinks that Bridget is still alive in Arkham, but says she shall go in on her own. Jim Gordon and Harvey Bullock arrive at Butch's mansion to talk with Tabitha, who states the sword Azrael had used was fake and that the real one is located at her grandfather's tomb. They later arrive at Gotham cemetery, where they receive the sword. Azrael arrives, injuring Tabitha and escapes with the real sword. Gordon warns Alfred over radio about Galavan, just as Bruce returns to the Wayne Manor. Gordon arrives, and shoots Azrael multiple times, until Cobblepot and Butch arrive. Butch fires an RPG, killing Azrael.

Gordon and Bruce question Professor Strange about Project Chimera, witch later makes Strange to send out Theo Galavan, now under the name of Azrael, who is sent out to take out Gordon. While at Arkham Asylum, Gordon bumps into Edward Nygma in the playroom. Nygma later overhears Strange and Peabody complaining about Gordon's interference. Nygma suggests that he can help them by taking out Gordon, but Strange refuses his suggestion. Bruce is told by Bullock and Gordon that their isn't enough evidence to imprision Hugo Strange. Azrael gets some memories back after looking over posters from Galavan's election. After that Gordon has been imprisoned by Nathaniel Barnes, lights flicker, and Azrael shows up, killing a little bunch of officers, and makes an attempt for Gordon, but doesn't succeed in it. Barnes and Gordon flee to a balcony, where Barnes fights Azreal with his pipe, and breaks his sword and rips of his mask, realizing Azrael's identity. In the end, Barnes is sent to hospital and Gordon leaves the GCPD by some distance, having Azrael watching over him at a bridge.

Bruce Wayne, Lucius Fox and Alfred Pennyworth search through the secret files on Thomas Wayne's newly fixed computer with the goal of finding a clue to who killed him and Martha Wayne, and why. Barbara Kean tracks down James Gordon. Claiming to be cured of her insanity, she tries to reconcile with Gordon but to no avail. Gordon discovers that the person who contracted Patrick Malone to kill Thomas and Martha Wayne is known as "the Philosopher". Bruce and Alfred track a lead from Thomas Wayne's computer and find Karen Jennings, a former Blackgate inmate who was experimented on at Wayne Enterprises by the Philosopher. She offers to identify the Philosopher, but the Philosopher sends Victor Fries to kill her. Following Jennings' death, Lucius Fox does further research and discovers that Hugo Strange is the Philosopher. After many failed attempts, Strange finally succeeds in resurrecting someone from the dead: Theo Galavan.

James Gordon continues to flee the law as he tries to clear his name. When Gordon secretly approaches Edward Nygma for help, he quickly deduces that Nygma framed him due to Nygma's suspicious behavior. Nygma electrocutes Gordon into unconsciousness, but Gordon awakes just as Nygma is preparing to kill him. Gordon asks Harvey Bullock and Selina Kyle to report to the GCPD. Gordon follows Nygma into the woods, where he is going to destroy evidence of Kristen Kringle's body. Nygma admits that he framed Gordon, as the GCPD eavesdrops on the conversation. They arrest Nygma before he can kill Gordon. Nygma is placed in Arkham Asylum. Nathaniel Barnes offers Gordon his job back, but Gordon declines, as he has other matters to deal with. Barbara Kean is released from Arkham Asylum after she stops showing any sign of mental illness. Following the death of his father, Cobblepot is bullied by his step-family. However, when he discovers that they killed his father, his former self returns and he murders his step-family.

Gordon is adjusting to life in Blackgate Penitentiary. Warden Carlson Grey (Ned Bellamy) announces to Gordon that he will be transferred to a new section, dubbed "the World's End", where the criminals Gordon arrested are sent, which is part of Grey's plan to kill Gordon. He's constantly aided by guard Wilson Bishop (Marc Damon Johnson). Gordon is told by Bullock that Lee has lost their baby and laid low. Later he is defended from attackers by convict Peter "Puck" Davies (Peter Mark Kendall), who is beat and sent to the infirmary. In an attempt to save Gordon, Bullock meets with Falcone. Gordon's death is successfully staged, and he and Puck escape. Puck dies from his bloodletting while Gordon is given a safe house so he can clear his name and find Lee. Meanwhile, Cobblepot reveals to Dahl about his criminal activities, for which Dahl forgives him. Dahl is told by the doctor that his heart defect is infected and given little time to live. Upset that Cobblepot may receive what they perceive to be "their" inheritance, Dahl's wife Grace and her children Sasha and Charles poison a drink for Cobblepot to ingest. However, Dahl drinks from the bottle and dies, after stating to Cobblepot his intentions of changing his will in favor of him.

Gordon and Bullock investigate a trail of clues left in a museum robbery, which, unbeknownst to them, were left by Nygma in a dangerous game of cat-and-mouse. Meanwhile, Gordon’s past comes back to haunt him when an anonymous person threatens to expose his hand in Galavan’s murder. Also, Penguin’s visit to some old friends leads him to meet his father, Elijah Van Dalh (guest star Paul Reubens), and Bruce practices his street smarts.