Season 1 ended with the mob war between Falcone and Maroni escalates but with Bullock's help, Gordon gets Falcone, Cobblepot, and Butch away from Maroni's men and to a safe house. When season 2 started Gordon is fired by Commissioner Loeb following his demotion for his role in Carmine Falcone's escape and Bullock resigns from the police. However, we all know how to determine Gordon is about cleaning up Gotham, so against his better judgement makes a deal with Cobblepot, who is now Gotham City's boss of organized crime. Cobblepot, who owes Gordon his life agree to help Gordon and pay Loeb a visit like only he can and forces her to reinstate Gordon as a detective and resign as police commissioner and Gordon, repays Cobblepot by collecting a debt from and eventually killing a strip club owner who owed the Falcone Crime Family money. Meanwhile, criminal mastermind Theo Galavan and his sister and enforcer, Tabitha Galavan broken out Barbara Kean and several inmates of Arkham Asylum including, Aaron Helzinger, Jerome Valeska, Arnold Dobkins, Richard Sionis and Robert Greenwood to join forces with him to wreak havoc in Gotham, except for Sionis, who is murdered for his refusal. And back of the Wayne mansion Bruce and Alfred discover a secret room at the end of the staircase, containing a note from Thomas Wayne advising Bruce to choose happiness over the truth unless.
Against Alfred wishes, Bruce tried to turn on his father’s computer but was broken by Alfred before he could turn it on making Bruce so mad, and he fired Alfred but changed his mind after Alfred agreed to train him to become physically strong. Alfred agrees to Bruce’s demand and seeks help from Lucius Fox to rebuild the computer. Meanwhile, Theo Galavan continues to execute his plan to take over Gotham and kidnap the mayor and places Jerome in charge of the other Arkham escapees, who now call themselves "the Maniax." The Maniax infiltrate the precinct and take down the GCPD, slaughtering nearly everyone in the building, including Commissioner Essen while Barbara Keen lowers Gordon away. Edward Nygma is wounded saving Kristen Kringle during the massacre. Following the massacre, Gordon seeks Harvey Bullock’s help and despite the wishes of his fiancée he reunites with Gordon and the GCPD in order to put an end to the Maniax's reign of terror.
Gordon and Bullock start searching for Jerome, as the few remaining member of the GCPD tries to recover from the massacre. Gordon and Bullock visit Jerome father’s house but arrives to find him being killed by Jerome, and Barbara has a romantic encounter with Tabitha. Theo Galavan reveals the next stage of his plan stating that his family built Gotham and that he will get revenge on those who stole the credit for doing so. Theo attends a charity event that Alfred, Bruce and Leslie Tompkins were attending with his plan in motion to keep the people hostage to prove his point that he can be a hero to the people of the city. Theo stabs Jerome in the neck and kills him, to accomplish his goal. Later Theo's kisses Barbara to make Tabitha watch and get jealous. Bullock pays a visit to Oswald Cobblepot, threatening to beat him if he approaches Gordon for a favor again.
GCPD has a new captain Nathaniel Barnes, who made it clear that he was there to clean up the police department and the city's corruption and made Gordon his new second in command. His first mission after cleaning house was to create an Alpha team with the best, brightest and toughest police trainees from the Police Academy. Theo Galavan kidnaps Cobblepot's mother and blackmails Cobblepot into murdering all of the possible candidates for the mayoral race so that Theo can run unchallenged. Alfred warns Selina to stay away from Bruce after what she did to Reggie. Bruce meets with Theo to thank him for saving his life and was immediately smitten by his niece Silver St. Cloud, and Theo informed him that she will be attending his school. Kristen Kringle and Nygma bond in a romantic “finally” and Captain Barnes informs the strike force that Cobblepot will be their next target.
A new villain arises after Gordon kills one of the Pikes brothers (an infamous family of arsonists) that Cobblepot hired to help with Theo request so that his mother would be released. With one of the brother dead they enlist their stepsister Bridgit for their mission to steal an old knife that belongs to the Wayne family. Cobblepot discovers the history behind the knife: in the 19th century it was used by Jonathan Wayne, Bruce's ancestor, to punish Caleb Dumas for his alleged sexual abuse towards Celestine Wayne, Jonathan's sister. After the Wayne's erased the Dumas name from history, the surviving members were exiled as punishment. They changed their names to Galavan, leading their descendants, Theo and Tabitha, to seek revenge on the Wayne’s by killing their last descendant, Bruce. Cobblepot plans to use this information to blackmail Theo and free his mother. Theo asks Gordon to endorse his candidacy for mayor, Gordon declines but late agrees to support Theo if he can help GCPD to clean up Gotham after an incident that got a member of the strike team killed.
Selina tries to help Bridgit to leave Gotham City, but as she was leaving, she got abducted by her step brother where they continued to abuse her. However, she could take it anymore and snapped and burned the pike brothers to death. Theo offers his assistant to help Bruce clean up the corrupted Wayne enterprises. Bridgit is badly injured in a struggle with the GCPD strike force but was pronounce dead because her entire body was burnt. However, she was later taken to Indian Hill where the underground division of Wayne Enterprises is where they secretly perform inhumane experiments on super-powered beings. Kristen Kringle learns that Nygma murdered Officer Dougherty, and Nygma accidentally strangles her to death in an attempt to keep her from telling anyone.
After chopping off Butch’s hand and sending him undercover at Theo’s HQ to help locate his mom he was an accept and cured of Cobblepot’s programming and leads Cobblepot to the location of his mother, where Theo Galavan and Tabitha Galavan are waiting. Cobblepot’s mother was killed in front of him by Tabitha, and they tried to kill him a well but her escape vowing to kill Theo in revenge. Now mayor Galavan he uses his power to convinces the GCPD and the public that Cobblepot assaulted him, and Galavan has Harvey obtain a warrant for Cobblepot's arrest. Gordon begins to suspect that Galavan is framing Cobblepot and tracks down Butch Gilzean, who reveal to him that Theo has been blackmailing Cobblepot and that he murdered Cobblepot's mother. Tabitha murders a member of the GCPD strike force and Both of Nygma's personality’s emerges as his condition worsen.
Theo gave Barbara permission to kill Gordon and made Bruce a proposition if he sells his controlling position in Wayne Enterprises to him and, in return, he would provide Bruce with information about his parent's killer and the culprits responsible. Barbara went to the GCPD to make her own proposition to Gordon and in spite the warning from his girlfriend Leslie Tompkins that it was a trap he still went along with Barbara’s plan. Gordon travels with Barbara to an unknown location, but the squad car is assaulted by Tabitha and her crew. Gordon wakes up in Gotham Cathedral, where he and Barbara were going to have their wedding before their break-up. The Strike Force discovers Gordon's location, thanks to the help of Bullock, Leslie is kidnapped by Tabitha. Gordon fights with Barbara, leading to Barbara hanging outside the church and falling, resulting in severe injuries. Following information obtained by Barbara, GCPD rescue Aubrey James from his abduction. Bruce declines Theo's proposition just as Gordon arrives and arrests Theo, who destroys the evidence on the Wayne’s' killer. Meanwhile, while trying to bury Kristen Kringle, Nygma discovered an injured and exhausted Penguin, who asks Nygma for help.
Bruce and Silver are kidnapped by Tom "The Knife" as a part of Selina and Bruce plan to have her reveal the name of Bruce's parents' killer she eventually told Tom that the killer's name is "M. Malone" but later claims that she lied. Galavan is released after Mayor James' lies, stating that Galavan did not kidnap him, framing Penguin instead. Gordon is captured by Theo, who reveals the history of his family to Gordon, but Gordon is rescued by Cobblepot and Gabe. Alfred grows suspicious of Bruce's whereabouts and searches Theo's residence, where he is wounded in a fight with Tabitha, which he narrowly escapes. Leslie notices Kristen Kringle's absence, but Nygma told her that Kringle left town with Officer Dougherty. Theo kidnaps Bruce, as part of the Order of St. Dumas' plan to "cleanse" Gotham.
Tabitha recruited a killer agency to put a bounty on Gordon’s head. After Theo had destroyed the information he claimed to have had on Bruce parent killer, Bruce turned Silver to find out what she knows about his parent killer. Alfred warns Silver to say away from Bruce, but he refuse and try to sneak out to see her and was stopped by Selina, who told him that she is not who she is pretending to be. Gordon and Barnes investigated Theo's condo for evidence and was ambushed, but they manage to fend them off, but Barnes is severely injured. Police reinforcements arrive but are eliminated by another hired killer named Eduardo Flamingo. An angry Gordon almost killed Flamingo but was stopped by Barnes, and Gordon arrests Flamingo, but, before being placed in his cell, Flamingo kills another officer. Meanwhile, Nygma persuades Cobblepot to move on from the death of his mother and the kill one of Theo's kidnapped henchmen in celebration. The Order of Saint Dumas arrives in Gotham City.
Gordon wakes up in Nygma's house only to learn from Cobblepot that he is now a fugitive from the law for assaulting Theo Galavan and never returning to the GCPD despite a documented arrest. Gordon and Cobblepot plan to break into Theo's residence and save Bruce Wayne. After being questioned by Barnes on Gordon's whereabouts, Leslie learns Gordon's location from Nygma. Leslie attempts to persuade him to turn himself to the GCPD by using her pregnancy news. Nygma informs Alfred, Bullock and Lucius of Gordon's location. Gordon, Bullock, Alfred, Selina Kyle, Cobblepot and his gang all arrive at Galavan's residence just as the Order of Saint Dumas is about to kill Bruce. During a clash between the Order and Cobblepot's gang, Order is defeated, Theo, Tabitha, and Silver St. Cloud try to make their escape. After being bullied by Theo, Tabitha and Silver escape but leave Theo behind. Cobblepot convinces Gordon that Theo might never be convicted, and the two take Theo to the docks and murder him. Gordon proposes to Leslie. Theo's body is discovered by Wayne Enterprises, who take the corpse to Indian Hill where Fish Mooney's body is also being kept. The scientists state that Theo's body is to be experimented on by Professor Strange.