An art show is taking place at the Gotham Museum of Art. A world-record holding bomb is on display when suddenly it starts counting down. The crowd panics and quickly leaves, and we see Edward incognito amongst the crowd. He steals one of the paintings and draws another green ? on the painting.
Barnes is briefing Jim and Bullock on the museum robbery. Barnes keeps Jim behind a minute to inform him that Internal Affairs is reopening the Theo Galavan murder file based on an anonymous tip. The witness says they saw Jim kill Galavan. Jim continues with his story. Edward wants to have his chat with Jim, but Jim promises him they will discuss Ms. Kringle later on.
Butch and Tabitha are hanging out when they are paid a visit by a rehabilitated Penguin. Penguin feels bad for how he treated Butch and wants to apologize to him. Tabitha teases Penguin about his mother and wants to kill him. Butch tells them to let Penguin go and that they are square. Tabitha is shocked but wants to punish him before he leaves.
Jim and Bullock investigate at the art museum. Jim tells Bullock the truth about IA investigating him. Bullock says he will talk to his friend Jenny inside IA to see what they have on him. They meet Mr. Thatch, the museum director, who shows them that the painting "Mad Grey Dawn" was stolen. He shows them the other two paintings that were defaced. The two French words mean Market Street. Jim thinks he was sending a message. They uncover a potential bomb threat and race to the scene.
Edward is opening his trunk and taking out the bomb. He is incognito again as Jim and GCPD arrive. They clear out the building and find a locker with another green ?. Edward clicks on the device and Jim takes it out and tosses it into the middle of the building as it explodes. Edward discretely sneaks away after observing his work. Barnes arrives and tells Jim this case is top priority. Edward tells Jim he will get him the forensics on the case and continues to plan his next move against Jim.
Selina and Bruce visit Ivy, who is working for the Gilzean gang that produces magic mushrooms. Selina intends to rob the gang and Bruce wants to help. He wants to discover who he is and not rely on his money. Ivy has slipped the most potent mushroom, called Blue Devil, into the gang’s lunch to knock them out. Bruce and Selina sneak upstairs to steal the money and Bruce convinces the man who wakes up that he is dreaming. They try to run away, but other members of the gang arrive and catch them.
Edward is plotting his next move at his house when his old friend Penguin pays him a visit. They talk briefly and Edward notices that Penguin has changed. He tells Penguin his new personality his currently hitting its stride and he is not a fan of this new and improved Penguin.
Sonny Gilzean is trying to locate his uncle and is holding Selina and Bruce. Selina taunts him and Bruce stands up to him, which leads to Bruce getting quite the beating. Bruce hears Alfred’s motivation in his head and fights back. Selina grabs some money and they are able to escape.
Penguin is visiting his mother’s grave. A man approaches with flowers and introduces himself as Elijah Van Dahl. He soon realizes that he is Penguin’s father. Elijah takes Penguin to his mansion, where he talks about meeting Gertrude and their relationship. He apologizes to Penguin for not knowing about him sooner and is happy to have him in his life now.
Bullock tells Jim his source in IA claims the witness saw Jim shoot Galavan. Bullock tells Jim he is going to be the primary suspect. Leslie and Jim are eating dinner and Leslie knows something is wrong with him. He tells her about the IA investigation opening up and he tells her that he can fix this.
Edward visits GCPD Officer Pinkney at his home. Edward gives him a riddle and then viciously attacks him with a crowbar. Bullock tells Jim the forensics on the bomb that it was trigged from a payphone. Jim visits the phone and finds it is right outside Pinkney’s apartment. He finds Pinkney dead on the floor. Barnes arrives and draws his gun at Jim. Jim tells him he was following up on a lead. Barnes tells him that Pinkney wanted to talk…about Jim. He tosses Jim handcuffs. He tells Jim he has to take him in.
Selina is stitching up Bruce, who tells her that when he was getting beat up, nothing else existed to him. He knew he was going to be ok and he knows that he will not be able to be broken. Bruce is quickly growing up before our very eyes.
Jim is being interrogated by Barnes. Jim claims he was set up. Barnes tells him that Jim’s fingerprints are on the crowbar. Jim keeps pleading his case and through flashbacks, we see that Edward stole the crowbar, he took the files from the report and he got Pinkney’s signature. Edward masterminded this entire setup of Jim. Barnes wants Jim to tell the truth and confess, but Jim refuses and wants his lawyer. Barnes calls him a disgrace to the badge and puts him in handcuffs and wants him taken to the county lockup. Jim tells Bullock that the bomber set him up. We see the true mastermind, Edward, watching as Jim is taken away.
It is four weeks later and the Jim Gordon murder trial is over. Jim has been found guilty and sentenced to 40 years in Blackgate Prison. Selina and Bruce hear the news on TV and Bruce feels this isn’t right. Barbara Kean finally wakes up at Arkham Asylum. The news yells for someone to get Hugo Strange. The Van Dahls welcome Penguin to their family, which seems to have something suspicious about them.
Leslie visits Jim in prison. Leslie wants to fight this, but Jim wants her to move on and forget about him. He wants her to raise their child in safety. He tells her to forget about him and that he will refuse any contact from her. He is only looking out for her.
Jim is being taken to Blackgate while Bullock rides along with him. Bullock promises Jim he is going to find out who set him up. “You were a good partner, Harvey,” Jim says as he is taken inside. “I still am…” Harvey replies as he watches Jim being taken inside.