- "Hugo Strange would rather destroy half the city than let them out. And now they're out."
- —Jim Gordon to Harvey Bullock
The GCPD Strike Force arrives at Arkham Asylum, ready to blow the gates. Suddenly Basil, disguised as Jim Gordon, appears before the police to stop them, claiming that nothing bad was happening there. In basement of the Asylum, Hugo Strange prepared a bomb to blow up the Indian Hill facility, and enlists Ms. Peabody to prep the patients for transfer to the upstate facility.
Meanwhile, Bruce and Lucius are at the mercy of Edward Nygma, who tries to find out everything they knew about who ran Indian Hill. On the other hand, Professor Strange administered a truth serum to Jim to find out what his plan was and told him that he could relax. Meanwhile, Basil reaches the GCPD trying to impersonate Gordon, but Bullock asks him whether he was feeling alright, noticing that he was acting different. At the same time, Lucius suggests the answer to Nygma's question was Hugo Strange, though Bruce gave the answer of Wayne Enterprises, which was correct. Nygma then asked them who ran Wayne Enterprises.
When the transfer process starts in Indian Hill, Fish Mooney tries to touch Ms. Peabody to control her, but fails. Meanwhile at Elijah Van Dahl's mansion, Penguin, Butch and Barbara hear the recent developments about the raid on Arkham. Back at Arkham, Hugo questions Gordon on several things, answering guilty for most of the questions. Hugo then absolved Gordon of all of his guilt, taking away the weight of his burdens. After successfully relaxing Gordon, Hugo questions Jim on whether he knew who controlled Gotham behind the scenes, though Gordon tells him that he doesn't know. After revealing that he didn't know anything at all, Jim tells Hugo that he should have went after Leslie. Afterward, a timer goes off, and Hugo tells Jim that he has a few hours to live before he leaves.
On the other hand, Lucis and Bruce give an incorrect answer about who ran Wayne Enterprises, and Nygma activates the poison gas, laughing as the two fell unconscious. While unconscious, Bruce has several flashbacks. Both Lucius and Jim later wake up in the same room as Jim. There, Jim apologizes to Bruce for making the oath to find his parent's killer in the past. At Arkham, Ed reports his achievements to Strange, and although he offers to assist Strange with any of his other cases, Hugo has him locked in his cell. Later Hugo contacts the white-haired woman in an owl mask, and reports his discoveries. She orders him to kill them all, and to continue with his patient's transfers. She then reprimands him for releasing Galavan, and told him that none of his other patients were to be seen, at any cost. At the GCPD, Basil's attitude while impersonating Jim begins to generate the suspicion of both Bullock and Alfred.
Back at Indian Hill, Selina meets with Bruce, and having manipulated her Bruce apologizes and tells her to escape. On the other hand, Ms. Peabody attempts to use thorizine on Fish to transfer her, but she fails and falls under the control of Fish's powers. Minutes later, when Hugo Strange discovers Fish's new powers and that Ms. Peabody was under her control, Strange attempts to stop her from escaping. He then flees from Fish's touch, and Fish orders Peabody after him. Hugo goes to activate the bomb and Peabody tries to prevent him from activating it, but he knocks her unconscious and activates a lockdown on the facility.
At the GCPD, Alfred remarks on Basil's weird behavior, and Barbara visits the GCPD station to ask Jim what was happening at Arkham. However, after noticing his behavior, she realizes that he wasn't Jim. Barbara immediately hits him and the whole department watches as Basil's face becomes deformed due to the hit. Meanwhile, Hugo Strange meets with Victor Fries and Firefly, accompanied by Selina, entrusting Fries to kill the remaining prisoners. After Selina objects, Strange orders Freeze to kill her, but Bridgit stands to protect her. While Mr. Freeze and Firefly fight, Selina takes the opportunity to free Bruce, Lucius, and Gordon. All go to the site of the fight where the group witnesses Strange trapped in the middle of Freeze and Firefly's battle. After being hit with both ice and fire, and knocked unconscious, Gordon checks to see if Strange was alive. Below Arkham, the bomb timer counted down. At the GCPD, Barbara informs Penguin of Hugo Strange attempting to escape Arkham, and Cobblepot thanks her and tells Butch to get ready so they could catch him.
When Strange regains consciousness, he completely rules out going down to the facility, as he had set off a bomb. Lucius notes that a radioactive material had been detected down there, and Strange told him he didn't have enough time. However, Strange told them he had calculated the risk of a radioactive cloud was relatively low. Hugo then told them that paying the price of thousands dying was better than releasing the monsters in the facility. After refusing to take them down there, Selina told them that Nygma knew the way down to the facility. Ed then shorts the security system, and Lucius and Gordon make their way into the elevator. Down in the facility, the door opens and Fish Mooney makes her way to the bus, driving it out of the Indian Hill facility. At the bomb site, neither Gordon or Lucius had an idea of how to defuse the bomb. Elsewhere, several patrol cars sped to Arkham and Fish continues to drive the bus. Lucius and Gordon aren't able to manage to come up with an idea on how to diffuse the explosive until suddenly Peabody regains consciousness and tells them "water." With a few seconds left on the timer, Gordon throws water on the circuits of the bomb and it miraculously turned off, afterwards, he and Lucius realize that Mrs. Peabody was actually asking them for water for her to drink. Elsewhere, Fish drove the bus away from Arkham, and she is pursued by a GCPD patrol car. In Arkham, Nygma screams in his cell asking what was going on.
Outside Arkham, Hugo Strange was put into a police car, and Bullock commended Jim for defusing the bomb. Gordon then informs Bullock that Indian Hill's residents were gone, and Bullock told him that several patrol cars were in pursuit of a bus that left the Indian Hill compound. Meanwhile, Fish continues to drive the bus, evading the GCPD patrol cars. Back at Arkham, Gordon tells Bullock that monsters were on the bus. Back in the city, Fish crashes the bus after being shot down by Butch Gilzean, Penguin, and his men. While walking up to the bus to confront Strange, Penguin is surprised to see Fish alive and well. At Arkham, Bullock orders GCPD officers to find the bus. Gordon then tells Bruce of his intention to leave the city to find Leslie. After that, Bruce tells Alfred of the secret council that controlled everything in Gotham, and that they were close to the ultimate truth. Bullock managed to catch Jim before he left, and Gordon reassured Bullock that he had everything under control, before leaving in the latter's car. Elsewhere in the city, a homeless woman notices the crashed Indian Hill bus while walking the streets. Hearing their moans, she opens the door to release them, and to her horror, monsters begin to walk out. A boy identical to Bruce Wayne, but with longer hair, thanks her before walking away.
- The episode is dedicated to production designer Doug Kraner, who had passed away on April 4, 2016.
- The figures created by Hugo Strange who are unleashed at the end of the episode are a reference to the Monster Men in the comics.
- 514A is introduced in this episode.
- This is the only season finale where Morena Baccarin (Lee Thompkins) does not appear.