- "Your father started Pinewood, Bruce. His intentions were good. But the man in charge took advantage of him. He didn't realize the truth until it was too late. Pinewood was his burden. But it doesn't have to be yours."
- —Karen Jennings to Bruce Wayne
After leaving Arkham Asylum, Barbara attempts to make amends with Gordon. Then, Bruce and Alfred track down one of Thomas Wayne's former friends from Project Chimera, but Hugo Strange disrupts their plans.
At Gordon's apartment, he is visited by Barbara Kean. Immediately he points his gun at her and demands to know what she was doing there as she was supposed to be in Arkham Asylum. Barbara tells him they let her go because she was completely sane and regretted all the crimes she had committed. As such, Gordon dismisses her, but while she was leaving she notices he was investigating The Lady in correlation to the Wayne murder case. Though she offered her help, Jim rejected her offer. Outside, Bullock arrives with a Pizza and beverages and is surprised to see Barbara free. At Wayne Manor, Bruce looked through his father's computer, and Alfred arrived down to the lair to inform them that he had prepared a meal upstairs, much to Lucius' pleasure. However, on Thomas' calendar Bruce discovers that he had scheduled a meeting with a woman named Karen Jennings about something called "Pinewood Farms" the same week he was killed.
With the intention of finding The Lady, who had fallen into disgrace after Jim killed her elite team, Jim prowled the streets of Gotham brutally attacking many criminals to find out her whereabouts. After interrogating many men, he discovers that The Lady was at a nightclub called Artemis.
Meanwhile at the Indian Hill facility, Hugo Strange, watches as Theo Galavan is prepared for reanimation when notified by Ms. Peabody Peabody that someone in Wayne Enterprises was seeking information about Karen Jennings and Pinewood Farms. Wasting no time, Bruce and Alfred arrive at Karen's cabin in the woods where inside they are surprised to discover that Karen had a reptilian claw instead of a left hand due to an experiment.
At Artemis, Gordon tries to enter but is denied entrance as it was a members only club. Unexpectedly Barbara appears and offers help to knowing how much he cared about the Wayne case. Inside, Barbara approaches to The Lady.
When Karen learns that Bruce is the son of Thomas Wayne, she reveals that Pinewood was a bioengineering program of Wayne Enterprises in which she served as a volunteer after being sentenced to Blackgate Penitentiary after accidentally murdering her abusive father. Though Bruce considered this an act of self-defense. Promising to fix her crippled hand, Karen was instead given her claw. When Thomas discovered what they were really doing at Pinewood, he closed the program immediately and paid to hide all the survivors of the program. Bruce then deduces that the program had been started up again, and demands that Karen takes him to the original Pinewood facility.
Back at Artemis, Barbara eventually gains The Lady's trust, and Jim tries to sneak into the club through the kitchen area, but is caught. As he suspected, Barbara betrays him and subdues him, putting him in the capture of her and The Lady. Soon after, Jim is tied to a chair where The Lady, motivated by Barbara before killing him, reveals that she sent Matches to kill the Waynes at the request of an employer who never revealed his true name, but identified himself as the "Philosopher." Having got what they came for, Barbara zaps The Lady with an electric baton and helps Gordon to escape.
At the Pinewood facility, Bruce, Alfred, and Karen investigate inside the building, but are chased by two assassins sent by Hugo Strange to capture Karen. While escaping, she kills one of her pursuers with her claw, while Alfred shoots the other. Unfortunately, when they finally escaped outside they were stopped by the police where they also see Karen's clawed hand.
Outside Artemis, Barbara tries to make Gordon see that everything she had done, she had done for him, but Jim tells him he could not forgive her because she tried to kill Lee. Afterward, Jim is called by Bruce who hastily explains the situation, and Gordon leaves to meet him.
Soon after, Gordon reaches the GCPD and is informed of Alfred's arrest. He discovers that Bruce was in Nathaniel Barnes' office talking to him. After Bruce tells Barnes everything that happened, Barnes orders that Karen be sent to Blackgate.
At a diner, Bruce informs Gordon of what they had learned, and Gordon shares his suspicions that he suspected that the Philosopher was in charge of Pinewood, so he quickly begins to plan a way to prevent Karen from being sent to Blackgate since she was the only person who could identify him.
At the Indian Hill facility, Strange is notified of Karen's arrest, so to deal with the situation Strange decided to release Victor Fries to test out his new cryogenic suit that the Indian Hill scientists made so that he can move around in warmer temperatures.
After Gordon, Bruce, and Alfred hijack the armored truck that was carrying Karen and bribe the driver to remain silent, they start heading for Wayne Manor. Inside the truck, Karen tells Bruce that Thomas used to visit her frequently and treated her as if she were his daughter. However, she also reveals that his father was the one who initiated "Pinewood Farms" and although he had good intentions "The Philosopher" took advantage of him. Unfortunately, the truck was stopped as the street was covered in ice, an ambush created by Victor Fries. Outside, Gordon and Alfred attempted to subdue Fries, though they failed. Seeing that everyone was in danger because of her, in the end, Karen decides to sacrifice herself and approach Fries, who freezes her and breaks her body into pieces. Fries then throws a cryogenic grenade at Bruce, Alfred, and Gordon. While they run for cover, Fries escapes.
At Butch and Tabitha's home, Butch arrives to see Tabitha comforting Barbara who was asleep on their bed.
Back at Wayne Manor, Bruce wonders how to move forward because Karen was the only lead they on identifying "The Philosopher." However, Lucius Fox arrives with an important discovery after having sought scientists who had worked for Wayne Enterprises cross-referencing the words "Pinewood" and "philosopher". To the astonishment of the group, Fox showed them a photograph of the old Gotham cricket team where Thomas stood by his friend Hugo Strange, otherwise known as " The Philosopher ." Bruce takes this discovery with extreme displeasure after discovering the fact that his father's death was ordered by one of his friends.
At Indian Hill, Ethel Peabody informs Strange that Fries had seen Gordon and a boy, who Strange deduced was Bruce Wayne, while killing Karen. Suddenly, they are alerted by an alarm in the room about Patient 44. Upon arrival to the Indian Hill facility they see a resurrected Theo Galavan brutally attacking his medical examiners and orderlies, and recites lines from the Order of St. Dumas, screaming "Azrael" towards the end.
- At the end of the episode Theo Galavan quotes the name Azrael. In the comics Azrael is an assassin created by the Order of St. Dumas and made his first appearance in Batman: Sword of Azrael #1.
- Like several episodes before it - notably "Rise of the Villains: A Bitter Pill to Swallow" and "Wrath of the Villains: Mr. Freeze", graffiti featuring eyes with "HAHAHAHA" painted under it in red to give the impression of a smile is a clear nod towards the Joker.
- It is shown that the month Thomas and Martha Wayne were killed was June.