Nygma and Oswald square off in their jail cells. Nygma doesn’t believe Oswald is alive. Penguin says that Nygma gave him something to live for, revenge. Nygma then smacked Penguin in the head, making sure he was real. He says not to call him Ed anymore, and that he became The Riddler when he “Killed” Oswald. The two jaw back and forth, both vowing to kill the other one.
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The alarm is going off inside Wayne manor, and Dopple-Bruce is looking around the study. Selina appears and tries to kill him. DB stops her, and says he’s glad she’s alive. Db says he was forced to push her because she was going to tell Alfred. As they fight, Alfred enters. She says, “He’s not Bruce!” DB knocks her out, and Alfred notices he’s been stabbed. He knows he’s not Bruce because he doesn’t feel anything. DB says Bruce is “serving a greater purpose than himself. As am I.” DB attacks Alfred, gets him on the ground, and knocks him out with a pole.
The Shaman and Bruce pull up to a stone mansion, and get out of a car. The Shaman says “Welcome home” and Bruce looks out over the City of Gotham.
Lee is sleeping by a fire, and she’s awoken by Mario. She said she’s had a terrible dream, and she tells him all about the virus that brought out the “Dark part of him.” Lee then says Jim shot Mario on their wedding night. He then slits his wrist, lets his blood pour into her wine glass. He tells her to drink and Lee wakes up, alone.
Jim and Harvey are talking about the court’s bomb at the GCPD. Jim is looking over a set of blueprints, talking about an extra 2000 square feet in a building that wasn’t documented. They head out to find it.
In the basement of the building, Jim and Harvey investigate with flashlights. Jim notices a hidden door in the wall, and Harvey accidentally opens it with the breaker. The room they find inside is vast, but mostly empty. All this they find is a crystal owl statue, that illuminates the Gotham city blueprint when light shines through it. A bomb comes in, they duck, and it explodes. Barnes enters, in a full super-suit. With an axe on one hand, he knocks Jim out, saying he has come to fulfill his promise.
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Alfred is on the phone, trying to get in touch with Jim at GCPD. Selina sits on the chair, ice pack on her head, as Alfred hangs up. He asks if she can remember anything more about DB, and she recalls everything about the clone and the judgement. She doesn’t think the real Bruce is still live, but Alfred knows he is. He says she’s going to help him, because he’s been a friend to her. She doesn’t know what good it will do her. He says she’s just like her mom, and she should run away, never returning to Wayne Manor.
Harvey is in the room, and a witness says he saw Barnes leave in a meat truck.
Penguin is trying to carve a knife on the cell floor, and Riddler says he’s not doing it right. The two argue about his name, and Penguin continues to call him Edward. Riddler says Penguin is pathetic for hanging onto their relationship. Oswald says he’s not there because he didn’t love him back, he’s there because Edward killed him and took down his empire. Edward blows a dart into Penguin’s neck, and the latter begins to choke. This is when Nygma makes his escape, because Penguin can’t make noise. As he’s about to leave the cell, Penguin slams his food tray on the ground, making enough noise for the guards to come in. They enter, catch Riddler, and beat him.
Bruce and the Shaman sit opposite one another, on the floor, in a room with little furniture. There is one final step for Bruce to take, he has to take away the pain of his parent’s murder. The two go into Bruce’s mind, and the Shaman stands at the safe. Bruce has to be willing to put the pearls in the safe, so he can be free of the pain. He can become the protector Gotham needs. Bruce approaches the safe, but he refuses to put the memory away. He wants to, but he can’t. Then the Shaman says it’s time he told Bruce the truth.
Jim is chained to a chair, Barnes and Katherine in front of him. She says he could have played a pivotal role in Gotham’s future. She knows about the key card, and about Strange. She asks who else he spoke to, and he brings up what the Court did to his father and uncle. He yells at Barnes, saying he used to stand for something. Katherine says Barnes knows, as she does, that Jim is an enemy of Gotham. Barnes walks up to a podium, it’s clear they’re in an old court room. She leaves Jim alone with barnes, saying he won’t be around to see Gotham fall. Barnes starts a “Trial” for Jim.
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At Arkham, Lee talks to Mad Hatter, and he tells a rhyme about her late husband. He says she doesn’t look like herself, and he knows she hasn’t been sleeping. She says she didn’t blame him for Mario, because you can’t blame a lunatic. She asks why he infected Mario, and he brings up the Tea Party where he shot Valerie. He says he could tell that she loved Jim because of the way she looked at him, and Jim Gordon didn’t deserve love. So, he infected Mario to move her to hate Jim. He says she is really to blame because she’s the one who loved Jim.
Penguin wakes up in his cage, and Nygma yells at him. His lock pick was taken, and now they’re both stuck in captivity. According to Nygma, the court is planning some attack on the city. Penguin proposes they help each other escape, because neither one can kill the other while they’re locked away. They set ground rules. including a six-hour window after they escape where they can’t kill each other. Both men agree, and shake hands.
The Shaman gets out hit tools, and he tells Bruce it’s time to revel “his truth”. The two go into the subconscious and they stare at a fire. They’re watching something unfold at the Court of Owls. The Shaman is seen across the room, in a suit, standing over another member of the court. This member is in a mask, and on his knees. The cowering man is revealed to be the killer of the Wayne’s. Past-Shaman kills the man. He tells Bruce that the Court was a means to an end, a way to keep order in Gotham. He says that the Court’s day is over, and they must pay for their crimes. He asks Bruce to help him take the court out.
Barnes puts the axe back on his hand, telling Jim that they could have cleaned the town up together. He says Jim stood against Justice, and jim pleads guilty to shooting Barnes. The man says Jim’s punishment is beheading, to be taken out immediately. Jim starts trying to tell Barnes about the Court’s plan, about the bomb. It will affect the innocent and the guilty. Barnes says the virus is a gift, not a curse. Barnes reveals Lee came to speak with him, and she didn’t understand what the virus truly was.
Jim says he wants to die wearing his badge, he deserves at least that. Barnes allows it, and walks over to give the badge to Gordon. When he gets close, Jim pulls a pin from Barnes’ super-suit, sending a missile into the wall. Before Barnes can attack again, the GCPD enters. Barnes leaps out of the window and onto a car below. He gets up and runs away.
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Back at the station, harvey asks about Barnes, but no one has a lead. Jim says he’s going to Katherine’s house, hoping he can get there before she knows he’s free. Harvey says a team already has her in custody, and she’s being brought in. Alfred appears, asking Jim where he’s been. He tells Jim that Bruce has been abducted, and he starts to describe the Court of Owls. Jim then reveals everything about the Court that he knows. Then Alfred tells them about DB, and that he was created in Indian Hill. Alfred then talks about the Crystal Owl that he broke, and Jim needs to put it back together so they can find Bruce and the bomb. Alfred goes to get the owl.
Nygma has a knife to Penguin’s neck, and the latter is screaming for the guards. As they enter, Nygma slits his throat and Penguin falls to the ground. Red is coming from underneath his fingers. As he falls, and the guards examine him, they realize it was jell-o. The men take out the guards and Penguin starts to unlock them. They escape.
Katherine is brought into the GCPD, and she comes face to face with Gordon. He starts to investigate her about the bomb, and about Bruce Wayne, and she denies everything. She played Jim, revealing that she isn’t actually the leader of the Court.
Alfred brings the pieces of the owl to Harvey, and they call on someone to come help them put the pieces back together. Alfred leaves to go confront Katherine, and wants to know where Bruce is. He sticks a knife through Katherine’s hand.
Barnes arrives back at the station, in his new suit, saying “Court is now in session!” He throws a gas bomb into the crowd.
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Alfred has the knife in Katherine, saying he will gut her and stab her other hand unless she tells him where Bruce is. They hear rumbling, and Harvey goes out into the pit. Barnes has destroyed everything, using knock out gas. harvey says they all need to leave, and take Katherine with them. They try to escape, sneaking by Barnes. He’s giving a speech in the smoke-filled room. He drops rom the ceiling, knocking Jim out. All three men try to take him out, but bullets are bouncing off of him. Katherine demands he stop this “nonsense”. Immediately, Barnes uses the axe to cut off Katherine’s head!
He says it isn’t nonsense, it’s justice. As he is about to deliver the final blow to Jim, he blows off Barne’s axe-hand with a shotgun. Jim then knocks out Barnes.
Penguin and Riddler escape out of the prison, and into an alley. They scare off homeless people, and both drop their weapons honoring their agreement. Nygma asks how he will win, because Barbara is on Nygma’s side. Penguin says he has an army of Strange’s monsters. They part ways.
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People are cleaning up the station, and Lee comes back to the station. She and Jim talk and she says she is done with the GCPD. She says Barnes discovered the truth, “there is no justice here.” She says Jim isn’t willing to pay for what he’s done, but she is. Jim tells Harvey that they need to find out the location of the bomb, and he reveals that she wasn’t the leader of the court. However, neither man knows who is.
Bruce and the Shaman still sit on the floor, facing one another. They are in the subconscious, and Bruce faces the safe with his mother’s pearls once again. The Shaman says the court must pay, and this is the only way. Bruce puts the pearls into the safe, crying. The Shaman shuts the safe door, and thanks Bruce. back in the real world, the Shaman asks how Bruce feels about his parents’ murder. Bruce says he feels nothing. A man is in the corner of the room, and he is wearing a black owl mask. He says this is what the Court calls a ‘Talon’, someone who the Court trains to be a warrior. They pull boys from orphanages and turn them into assassin’s. He tells the man to cut off the smallest finger on his left hand, and the man does so without hesitating. He says Bruce will now become the perfect weapon because he will do whatever the Shaman says. Bruce agrees.
Back at the station, the owl crystal has been put together. They are getting ready to assemble a team to head out, but Harvey is told that Barnes escaped custody once again. He’s told there’s more, and that the virus sample from Strange is missing. Jim says Lee has the sample, and she is seen looking it over at her table. Lee loads up a syringe, and injects it into her arm. The virus sweeps over her face, and she smiles.
