The Court of Owls meet, and Kathryn says that the City of Gotham has fallen ill. Drastic action must be taken, and there is a new weapon that can destroy Gotham, so it can be rebuilt by the court. A unanimous vote is needed to pass the vote, ad all members, including Frank, decide Gotham must fall.
In the snowy mountains, Bruce lays asleep on the ground of his cell/room/ As the door opens, he wakes up, and sees a man in the doorway. Bruce asks to speak with whoever is in charge, and the man steps into the light.
The man says that the Court of Owls is a tool, and that the clone is in Gotham pretending to be Bruce. The man says that, by the time Alfred figures out the clone is around, he and Bruce will have accomplished their goals. He asked Bruce to eat, and that they will begin soon, and then leaves.
Jim is back at GCPD, and a TV shows that Aubrey James is the mayor again. Jim is acting odd when Harvey asks him about his uncle's cabin. Harvey talks about Nygma, and says that they haven't heard from him since the stairwell incident.
Jim is looking at the file of Michael Ness, the drunk driver who supposedly killed Jim's father. The man was killed in prison a few months into his sentence. The autopsy revealed that Ness had chronic liver inflammation. Harvey says if the man had consumed any alcohol, he would've been dead before he ever took the wheel. If that's true, someone messed with the report.
Jim asks Harvey to do some digging, and he leaves.
Ivy brings Penguin into her greenhouse in a wheelchair. It's clear that she's babying him a bit. She reveals that the plants are her friends, and that they helped bring Penguin back to life. As she hands him some broth, he throws the mug on the ground and says that he needs to get back to Gotham and start building an army.
Penguin tells Ivy to get a message to Gabe, and that he's a loyal soldier. Every army starts with one loyal soldier. ivy agrees to take the message.
Jim stands at his father's grave, and Uncle Frank approaches. Jim reveals that he may believe Frank about what happened to his Father. Frank tells Jim about the weapon on its way to Gotham, and he reveals the high-ranking fanatics in the Court of Owls are ready to destroy the city. He says he's going to find out what the weapon is, but Jim has to stay out of the way in case Frank is discovered.
Lee stands at her fiance's grave, and Jim sees her. He apologizes, and she asks about Frank. He says they recently re-connected. Lee says she's been coming to the cemetery a lot. She tells the story of an old man, who often smiles at his wife's grave. They got to spend an entire life together. Jim again says he's sorry. Lee asks him how he moves on, leaving destruction in his wake, and she walks away.
Harvey calls Jim, and says the man who killed his father was a life-crime kind of guy. The plea deal that got Ness out of prison was paid for by Carmine Falcone.
Gabe is hugging Penguin at the greenhouse, and he says Barbara is running things. He agrees to help Penguin build an army, and he's going to begin by telling all of their people that Penguin is still alive. Ivy says she doesn't trust him, and she puts on her truth-telling perfume to prove that she's right.
Penguin responds by saying that he doesn't trust Ivy, and that he wants nothing to do with her. She's upset, as she thought they had become friends. he says she is a "bit of a freak", and she leaves.
Gabe then knocks out Penguin, and calls Ivy a "smart girl" for not trusting him.
Bruce is seen in his cell, and he has a bowl in hands. The door opens again, but no one is there. Bruce ventures out into the hallway, looks around, and then takes off running. He runs throughout an array of halls, turning in multiple directions, and ends up back where he started. The man from earlier is now in his cell, asking if the can begin.
Bruce continues to try and run, but he keeps ending up back where he started. The man tells him that everything is a maze, but they need to realize their place in it. He tells Bruce that it's time to pick a direction, and finally escape the maze of life.
"Let me show you what I have to offer."
Jim shows up at Falcone's house, and the two square off about who they have lost. He confronts Falcone about the drunk driver, and asks if he ordered the hit on his father. He does, however, admit that the Court of Owls ordered the hit. Jim asks Falcone if he's a member, but he says they are only business partners. Falcone says that we all work for the Court, whether we know it or not. He says Frank is the one who ordered the hit on Jim's dad.
Frank walks down a hall, and Jim appears with a gun to his head.
Frank pours a drink, and Jim asks about the hit. He says that Falcone has called the court, and they're suspicious. He also reveals that he is the one who ordered the hit on Jim's father. The Court was going to kill Peter, so Frank had no choice.
Instead of helping Frank take down the court, Jim tries arrests Frank for the murder of his father. Frank escapes, points a gun at Jim, and tells him the weapon will be arriving at Dock 9C. If he doesn't find it, they're both dead. He tells Jim to make his choice.
Penguin says he didn't think Gabe had it in him, as the thug has him tied up in the greenhouse. Gabe says he isn't going to kill Penguin, but that his "sales force" is going to auction off the right to kill him. Some men enter the greenhouse, and Ivy is seen watching outside. Another man appears behind her with a gun to her head.
Back at GCPD, Jim reveals everything about the Court, and the weapon, to Harvey. He says Harvey is the only one he can trust. Harvey thinks that he should investigate the docks, but he has his back either way. Jim says the raid on the docks has to be done under the radar, and no one can know they're involved. It's clear Jim has an idea about who to call, but Harvey doesn't like it.
A man is seen on his knees, handing money upward, like an offering. Barbara is seated there, and takes the money from him. She says it feels a little light, and hands it to Tabitha. Then, she knocks him out with her stilletto, and asks, "Who's next?"
The phone rings, and Barbara answers. He says, "Jim, what an unpleasant surprise. Do I feel a favor coming on?"
Bruce sits with the old man in his cell, and the man says he has been waiting for this for a long time. She shows Bruce a collection of needles, saying that they are keys to unlocking your mind and soul. The needles extend from themselves, and one goes into Bruce's forehead. As Bruce's eyes roll back into his head, he sees a vision.
Bruce and The Man are back in Gotham, where Bruce had said he wanted to return to. They are standing in an alley, and he sees his family. This is where his parents were killed.
As his mother and father approach, Bruce tries to call out. They don't hear him. The mugger pulls the trigger of his gun, and Bruce wakes up. The man says it was a memory, and that the mind can do much more than simply unlock said memory. He says that we are always inside our own minds, and that Bruce has never really left that alley. In order to accept the teachings in front of him, Bruce needs to learn to escape that moment in his past.
Bac in Gotham, Tabitha and Barbara are torturing a man who works at the docks. He says there is no Dock 9C, but Barbara breaks him. He says Falcone never even asked about that dock. He says something already came in last week, and the crate is across the room. She then asks about their contact info, because she would love an introduction.
Someone is over near the crates, and everyone turns their attention over there. Someone can be heard screaming, and a man appears. As the guns start to fire, the man, who wears an owl mask dodges the bullets. He kills people with his swords, while Barbara and Tabitha escape. He then kills the dock-worker.
At the greenhouse, the men are taking pictures of Penguin for the auction. Ivy is tied up next to him. She assures him that she will be fine, and the men head over to eat a dessert that one of them brought in from the car. Penguin agrees to be nice to Ivy, if she will help him escape.
She calls one of the men over, and asks if valuable information regarding Penguin would be enough to get her free. He asks what it is, and she says she will whisper it in his ear. She asks if he likes her perfume, and then agrees to do anything she asks. She orders him to kill all of the men. Ivy and Penguin tell the man to kill everyone but Gabe, and then has the man take Gabe's gun. They then order the man to untie them, so Penguin can shoot Gabe himself.
Penguin kills the slave man, and then puts the gun in Gabe's face. He says he will auction him off to himself, piece by piece.
At the Court, Kathryn asks what Falcone told Jim about their group. Frank says that the only thing he knows is that he ordered the hit on Peter. He says he doesn't know why Jim is looking into things now. Frank says Jim won't stop until one of them is dead, and Kathryn declares,
"James Gordon must be killed."
Harvey and Jim talk about Barbara's discovery. They say that the weapon is being guarded by the swordsman, and that the crate came from Indian Hill.
Frank calls Jim, and says they need to talk. Jim says the weapon is here, and Frank says they are running out of time. He needs to come to his house, and Frank is seen with a gun in front of him.
At the Greenhouse, Penguin is making Gabe bury the bodies of the other dead guys. They are arguing about loyalty, and Gabe was upset because he was passed over. Penguin asks if he could be loyal again, and Gabe gets on his knees and begs for forgiveness. Penguin asks Ivy to make Gabe smell her perfume so that he can truly be loyal. He truthfully says that he can't because he never was loyal. He only followed Penguin out of fear. He says no one ever respected him, and they only ever thought of him as a tiny freak with an umbrella. Penguin loses it, and kills Gabe with a gardening toll.
Jim shows up and Frank's house. He tells his uncle that the weapon had come from Indian Hill. Frank says the Court no longer trusts him, as he didn't know the weapon was even in Gotham yet. Frank then reveals that he is supposed to kill Jim.
Frank says he needs someone he can trust on the Court, and that Jim needs to join them. He says that Kathryn is going to call to ask if Jim is dead. He says that Jim needs to pick up, and say that he killed Frank because of his father's death. He tells Jim that only he can finish his father's work, and then reveals how proud his father always was of him.
Then, Frank turns the gun on himself, and pulls the trigger.
Bruce is sitting in his cell, and the door opens. He tries to take The Man by surprise, but he is caught. The man takes out a needle again, and makes Bruce watch his parents die once more. This time, Bruce tries to interfere, but the the mugger disappears as he moves toward him. In the vision, Bruce starts to fight with his mentor. The mentor easily wins, and then says, "I have so much to teach you Bruce. But your pain blocks you from who I need you to become, from who Gotham needs you to become."
Back in the real world, Bruce's lip is still bleeding from the fight. The man says that some consequences can follow you back into reality.
When asked what he wants, the man starts to say that, over the years, they have tried to stop the plague of crime that is constantly sweeping over Gotham City. They never succeed, because people are afraid and fear breeds hopelessness. Bruce doesn't believe he cares about the people of Gotham, but the man says that he does. He tells Bruce that Gotham needs a protector, and he's the man to do it. The man says Bruce is to become a symbol against fear, and Gotham can be reborn.
At the greenhouse, Penguin is burying Gabe. He says he lost his temper, and that's sorry. Both he and Ivy says that words have always been hurtful. He says he needs help to take over Gotham, and then Ivy revealed they can have an Army of Freaks from Indian Hill.
Jim stands at his father's grave, and he answers his uncle's phone. It's Kathryn, and he agrees to meet with her. A car is already nearby, waiting for him. As he gets into the back of the limo, the episode ends.