The Medical Facility, part of Arkham West, was one of the first areas where the Joker had managed to seize control during the early stages of his takeover of Arkham Island. The Joker's Henchmen and Arkham inmate, Victor Zsasz attacked Arkham West, and killed most of the security guards in the area. The convicts entered the Medical Facility through the Medical Foyer after they killed two guards outside. It was here that Harley Quinn relaxed after she took Commissioner Gordon hostage, and was seated behind the front desk.
Meanwhile, the Blackgate Prisoners received orders from the Joker to round up all the doctors in the Medical Facility, particularly Dr. Young. The convicts secured the Sanatorium, then entered the Upper Corridor, and killed the Arkham orderlies and security personnel on their way further into the Medical Facility. The convicts rounded up five doctors and held them in the Sanatorium. One doctor attempted to escape, only to be brutally "torn apart" by the Joker's men, and thrown into the water.
Batman was alerted to the Joker's move inn the Medical Facility by an Arkham guard who hid in the Arkham West Watch Tower, and headed to the Medical Facility to put a halt to it.
The convicts took Dr. Adrian Chen hostage in the Surgery Room, then captured Dr. Young in the X-Ray Room. They also secured the Patient Observation Room, and trapped guard Aaron Cash and Dr. Stephen Kellerman inside, with orders to fill the room with Joker Toxin and kill them both. Batman entered the Medical Foyer and found Harley Quinn with Gordon during Quinn's "me time", but was unable to reach them, due to the fact that his way was blocked by a security barrier.
Batman used Explosive Gel to blow up part of the Medical Facility's roof, and entered Maintenance Access. From here, he used an air duct tunnel to reach the Sanatorium, where five gun-toting convicts were holding four doctors hostage, and strapped two orderlies to electroshock therapy chairs to prevent escape. Batman defeated the thugs, liberated the doctors, and moved to the Upper Corridor.He proceeded to the X-Ray Room, where Dr. Young was being held by five armed henchmen within a locked office.
Batman sprayed Explosive Gel onto the walls, and detonated it, which blew the men off their feet and knocked them out.
After rescuing Dr. Young, Batman also proceeded to the Surgery Room, where Dr. Chen was strapped down in the center of the room. It proved to be a trap, as the Blackgate Prisoners dropped down into the room from above and Batman had to fight his way through them before he freed Dr. Chen.
Batman moved to Patient Observation, where he liberated Cash and Dr. Kelllerman. Batman proceeded back to the Sanatorium, and paused only briefly to deal with a "present" that the Joker had left for him: a knife-wielding henchman. Back at the Sanatorium, Batman regrouped with the four doctors that he'd rescued earlier, as Cash and Dr. Young arrived from the Upper Corridor. Young insisted on heading to the Arkham Mansion to save her notes, and Cash agreed to accompany her.
Meanwhile, three of the Joker's men arrived from the Morgue to attack Batman, who prompted the doctors to flee to the Patient Observation Room. After he dealt with the convicts, Batman used the elevator to reach Secure Access, where several Arkham orderlies and a patient were being tortured by Scarecrow's Fear Toxin. Batman watched them panic to the point of death through a window in an operating room, but was unable to help them. Iron bars separated him from reaching Scarecrow, who fled the scene. Batman eventually continued to the Lower Corridor, where a dead Arkham security guard was dragged and left as a macrabare marker which pointed Batman toward the Morgue. Batman, having been exposed to Scarecrow's Fear Toxin, imagined that the guard's corpse was instead that of Commissioner Gordon. Wandering into the Morgue in his drugged state, Batman imagined that the Morgue housed his reanimated parents, then his hallucinations turned into a full-fledged nightmare after Scarecrow pumped more Fear Toxin into the Morgue. Batman dreamed that the ruined Morgue was turned into a fearful dreamscape, where he had to avoid the fatal gaze of a giant version of Scarecrow.
After the effects of the Fear Toxin began to wear off, Batman left the Morgue, entered the Lower Corridor, and realized for the first time that all that he had experienced was not reality. After he was attacked by three Blackgate convicts, Batman followed a narrow hallway to the Experimental Chamber, where Harley Quinn was holding Gordon hostage inside a small room. The area around the room was patrolled by the Joker's men, who were under orders to kill Gordon if they saw Batman.
Using his stealth skills, Batman managed to defeat the convicts and Harley, but then found that the Joker had left him a surprise in another room: Bane, who was strapped onto hoses that Dr. Young had used to drain the Venom from his blood. The Joker sprung his trap, and returned to Bane his supply of Venom, with chaotic results. Bane attacked Batman, and was aided by several of the Joker's men.
The Medical Facility was heavily damaged during the following battle, and the Boiler Room was destroyed after the battle had weakened its foundations. Batman and Gordon fled to Arkham West, where Batman rammed Bane with the Batmobile and knocked him into the Gotham Bay. As Batman rescued more of the Arkham Staff, he told them to all go to the Medical Facility, as it was the safest place on the island.
The Medical Facility was further damaged by Poison Ivy as her mutated plants overran the island later, though its remains were recaptured by the GCPD as they retook control of Arkham Island after the Joker's defeat. It was then converted into a makeshift hospital for those injured during the Joker's takeover, including Cash and Louie Green. The holding cells in the Sanatorium were temporarily utilized to hold the recaptured patients, as the usual cell blocks had been heavily damaged during the riot.
- There is a head in a jar that can be seen in the Sanatorium in an office.