The episode picks up right where last week left off, with Barbara at Jim Gordon's door. She tells him she's been officially released from Arkham Asylum, and that she "tells the truth now." She says that coming out of the coma was like "waking up from a nightmare," and that she's better – sane – now. He says he's happy for her, but wants her gone, and kicks her out.
Harvey shows up with a pizza and beer, and sees Barbara in the hall for a little funny moment.
Down in the cave, Bruce is going through his father's computer as it works to decrypt the files. He finds that his father was supposed to have a meeting with a Karen Jennings about "Pinewood Farms" the week he died, and Lucius Fox thinks it's probably a cover name for another secret program, like Indian Hill.
Bruce doesn't want to wait, and leaves to go see her.
Jim and Harvey are officially back on the Wayne case, and he wants to find "The Lady," the one who sent the assassins after Jim. Gordon arms up and starts chasing down leads, bashing in heads and limbs of hitmen around Gotham City. He finally gets a lead, a club called Artemis.
At Indian Hill, Professor Hugo Strange and Miss Peabody are trying to reanimate someone dead – "Patient 44." Apparently Karen Jennings has claws and was one of their first experiments.
Bruce and Alfred arrive at Karen Jennings' home, a cabin in the woods, and Alfred gets attacked as she arrives. – scratched by her claw hand.
Bruce starts asking Karen questions, about his father, Pinewood Farms – "Do you not understand these people will kill you?" she asks.
Jim heads to the Artemis, but can't get in – it's members only, and in fact womens only. Barbara shows up and offers to help. "I was there when you first caught the Wayne case. I know what it means to you," she says. She wants him to be able to start over.
Barbara heads into the club and goes straight to The Lady, who lets her sit.
Pinewood Farms was a bio-engineering program at Wayne Enterprises. Karen volunteered for it when she was at Blackgate ten years before. She had a crippled arm, and her father beat her for it – she killed him in self defense but got sent away. When they offered to fix her arm, and wound up with a claw, Thomas Wayne found out, shut down Pinewood, and paid to hide the experimented-on people. Sadly, Karen doesn't know the names of the people who were running the facility, but says she'll never forget the man who was running it by face.
Barbara and The Lady have a chat at the club, where she says she lied and acted to get out of Arkham – which story is true? She says she wants to get into the assassination business and has just the thing to restore The Lady's reputation. Jim sneaks in, and Barbara holds a knife to his throat.
Barbara and the Lady have Jim tied up, and Barbara is acting crazy. She tells The Lady that he was looking for who hired the Wayne hit. The Lady says "The Philosopher" is the guy's alias, and Barbara says "See Jim? Told you I had a plan," and tazes both The Lady and her goon. Huzzah!
Bruce, Alfred, and Karen get to the old Pinewood Farms facility. It looks completely abandoned, nothing going on there since she left. Three men show up and start giving chase. As Bruce, Alfred, and Karen start to run away, she turns back – and slashes the neck of one of their assailants. Alfred shoots another of them, and they run outside – where they are met by a couple of police who hold them at gunpoint.
Barbara and Jim chat about her plan; Jim wasn't… thrilled with it. Barbara really wants Jim to believe the monster inside her is gone. When she woke up from her coma, she remembered the way he looked at her when he was trying to save her from falling out the window. He says she can try to be a better person on her own, but he can't forgive her for trying to kill Lee. Bruce calls Jim, and he leaves.
When Jim gets to GCPD, he finds Bruce in Captain Barnes office and Alfred in lockup. They leave together, and catch each other up on their investigations. Jim wants to break Karen Jennings out and show her pictures of scientists that worked at Wayne Enterprises.
Strange is checking on Patient 44, and things seem to be going well there. Peabody tells him that Karen Jennings was arrested, and he decides to send Victor Fries as his assassin to keep her from talking.
Karen's in a police prison transport. While it's driving along, a hundred dollar bill hits the windshield. There's a huge bag of money on the pavement, and the cop driving the transport starts gathering it up. Jim knocks the guard from the back of the transport, and grabs his gun. He goes around the van and tells the other guard to keep the money, drop the gun, and let it go – and she does.
Bruce, Karen, and Jim have a chat – yes, The Philosopher is the man that ran the Pinewood program. She also tells Bruce that he sounds just like his father – Thomas helped her a lot for years. She reveals that Thomas Wayne started Pinewood Farms, with good intentions, but "the man in charge took advantage of him."
The van suddenly hits some ice – uh-oh – and spins out. When they get out, they see Victor Fries – in full Mr. Freeze mode. Jim shoots at him but his bullets bounce off. Karen tells them to go "It's me he's after." She tells Bruce, "I'm so glad I met you, Bruce. Your father would be proud of you and the man that you've become. She runs out, and Mr. Freeze blasts her, freezing her solid, and with one swipe – shattered her completely.
Butch and Tabitha have a new house guest – Barbara. Hmm.
Bruce is having a hard time over Karen's death. "She died because of what you're pursuing," Alfred says. "There will be others." When Lucius was looking for scientists, he found a photo. Hugo Strange – The Philosopher, standing next to Thomas Wayne. "He runs Arkham now!" Gordon says. "A friend. Someone he trusted. That's not fair. It's not right," Bruce says with a determined look in his eyes.
At Arkham/Indian Hill, Strange and Peabody talk about what's happened. Bruce Wayne and Jim Gordon are working together, he realizes. The alarm goes off from downstairs – it's Patient 44. As Peabody and Strange get there, Patient 44 is beating down all the guards/orderlies trying to restrain him. He is back from the dead, and it's Theo Galavan.
"What now, sister?" Galavan mumbles. "Oh, the holy city, I see. The Saint will deliver us. Azrael. AZRAEL!"0comments