Pinewood

Gordon (Benjamin McKenzie) receives a visit from Barbara (Erin Richards). He holds her at gunpoint, demanding to know how she was let out of Arkham Asylum. Barbara states she's "sane" and regretful about killing her parents. Gordon dismisses her and kicks her out of his apartment where she runs into Bullock (Donal Logue). Gordon is currently investigating The Lady (Michelle Gomez) as the possible contractor of Matches Malone to kill the Waynes. He then brutally attacks many hitmen who serve her until one of them reveals she may be in a club called Artemis. Gordon tries to enter the Artemis but is denied. Barbara arrives and offers to get inside so she can retrieve the information.

While Barbara and The Lady bond, Gordon infiltrates the club until he's captured by Barbara. He's tied to a chair and taunted by Barbara and The Lady. The Lady reveals she sent Matches for an employer but the employer never revealed his real name except his alias, "the Philosopher". Barbara then tasers The Lady and she and Gordon escape. Barbara tries to get Gordon to claim she's sane but Gordon can't forgive her since she tried to kill Lee in the church. Bruce (David Mazouz), Alfred (Sean Pertwee) and Lucius Fox (Chris Chalk) discover in the computer a meeting Bruce's father attended to meet a woman named Karen Jennings about something called Pinewood Farms. Bruce and Alfred arrive at a shack where they discover Karen (Julia Taylor Ross), who has claws from an experiment. She reveals Pinewood is a engineering program from Wayne Enterprises. She was convicted to Blackgate for murder after causing her father's death when board members appeared and offered her to fix her crippled arm. Thomas Wayne soon found out about Pinewood, shut it off and hid everyone.

While experimenting on someone dubbed "Patient 44", Professor Strange (B. D. Wong) is notified by Ethel Peabody (Tonya Pinkins) that someone is tracking the Pinewood Farms program. Bruce, Alfred and Karen arrive at the Pinewood Farms facility but they're pursued by men sent by Strange. While escaping, Karen kills one of the men with her claw while Alfred shoots another. They're then arrested by the police. Gordon arrives at the GCPD where Bruce and Alfred are set free. Bruce reveals everything to Barnes (Michael Chiklis) but Karen is sent to Blackgate Penitentiary. They then plan on breaking her out. Professor Strange is notified of this and decides to release Victor Fries (Nathan Darrow) with a new suit and armor.

 Gordon, Alfred and Bruce hijack the armored truck carrying Karen and bribe the driver to remain silent. In the truck, Karen reveals Thomas visited her frequently and that he was the one to start Pinewood Farms, before the Philosopher took over the command. Fries arrives and ambushes them. Karen decides to sacrifice herself and Fries freezes her and then shatters her corpse. Barbara is shown at the mansion of Tabitha (Jessica Lucas) and Butch (Drew Powell) where Tabitha decides to let her live with them. Fox arrives at Wayne Manor and shows Bruce, Gordon and Alfred new information he discovered. He identified a photo of Thomas Wayne with many colleagues, including Hugo Strange, who is labelled as "the Philosopher". This leads Bruce to discover that Strange was the one to kill his father.

 In Arkham, Strange and Peabody are tuned in to an alarm which leads them to a risen Patient 44 brutally attacking the medicals. He's revealed to be a resurrected Theo Galavan (James Frain), who now dubs himself "Azrael"

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