Arkham Asylum Incident
Shortly after the Joker had seized control of the Intensive Treatment Center, security officer Louie Green and over a dozen guards were directed to Arkham East by the Joker, where their radios went dead. At least three security guards patrolled around the Arkham Mansion, and one was posted inside the Mansion Entrance Hall to prevent entrance. In the Records Room of the Arkham Mansion, six convicts intercepted Dr. Young along with two security guards, Zach Franklin and Aaron Cash. The two guards were taken hostage while Young escaped to her office. Batman arrived to free Cash and Franklin, while three convicts discovered Young's office and tried to break into it. Using the Ventilation System, Batman reached the North Corridor, where two cells were, one in which Amadaeus Arkham spent his last years. Meanwhile, many of the Joker's men had moved down the South Corridor, and secured the multi-level mansion Library. It was here that Dr. Young fled, and encountered an orderly and an unidentified member of security personnel, identified only as "Bill".
Bill attempted to defend Young, but all three were inevitably captured. Batman, meanwhile, had managed to defeat the convicts breaking into Young's office and learned from the security monitors that Young had taken her notes from her office safe and fled. Batman rushed to the South Corridor and then to the Library, and found the Joker's men tearing the area apart in search of Young's notes. Young herself had been taken to the Joker, who decided to use Victor Zsasz to torture the formula out of her. On the lowest level of the Library, Batman discovered Bill and the orderly tied up in front of a bomb, later revealed to have been a fake. Scarecrow, meanwhile, had proceeded to the mansion, and rigged the South Corridor with his Fear Toxin to entrap Batman.
Wandering around in a drugged state, Batman awoke from an intense nightmare in the Arkham Mansion's Clock Tower. The Dark Knight cut the rope of the bell and sent it crashing down to the floor below, which caused extensive damage to the mansion's East Wing Corridor. Zsasz was hiding in Warden Sharp's office, and tortured the formula out of Young. Zsasz used Young as a hostage, but Batman used a Batarang to knock him out. Young was killed by a booby-trap that was rigged in the Warden's safe while trying to retrieve the security codes. Harley Quinn took Warden Sharp through the mansion afterward, beat him brutally with his cane, and left several convicts to "hurt" Batman. Quinn took Sharp out of the mansion, and Batman left in pursuit.
Shortly after, the Joker loosed the more unsettled mental patients of the island, who ravaged the mansion grounds, but did not enter the mansion itself. The Arkham Mansion suffered extremely heavy damage when Poison Ivy's Titan-enhanced plants overran the island. Aaron Cash and Zach Franklin regrouped with doctor Kevin Liew and a third surviving security guard in the mansion's Main Hall. The mutant plants, however, smashed through the mansion's windows and killed the third, unidentified, guard.
Batman returned to the Arkham Mansion shortly after, and found Cash and Franklin standing around the plants and Liew seated behind a desk. The Arkham Mansion's Entrance Hall was so overrun by Ivy's plants that the hall became filled with toxic spores released from the mutated vegetation, and Batman warned Cash to stay away from the plants as they would most likely kill him. The remains of the Arkham Mansion were retaken by the GCPD as they recaptured the island.
Arkham City Incident
After Arkham City Incident
Months after the death of the Joker, Scarecrow held a meeting at the Arkham Mansion, and invited all of Gotham's super villains to discuss a plan to take down Batman. Most of them agreed, but Poison Ivy wasn't fond of the idea, and was locked in a glass cell inside of a penthouse in Chinatown.
Arkham Knight Incident
After Batman defeated The Arkham Knight and saved the GCPD Building with the help of Oracle, Scarecrow captured Robin, and took him and Commissioner Gordon to the Arkham Mansion. Scarecrow told Batman to head to an empty warehouse on Miagani Island, where Batman surrendered his Utility Belt, and got into the back of a truck, which started heading to the Arkham Mansion.
Upon arrival, Scarecrow dragged the trapped Batman through the halls of the abandoned asylum, similarly to how Batman had brought Joker two years earlier. Finally having Batman at his mercy, and strapped to a gurney, Scarecrow forced Gordon to unmask Batman, and threatened to kill Robin if he refused. Batman, revealed to be Bruce Wayne, was struck with a concentrated dose of Fear Toxin, which finally allowed Joker to take over. While Scarecrow taunted Gotham's citizens and the world, Bruce was going against Joker inside his own mind. As Scarecrow told Batman about the upcoming carnage, Batman simply responded how he was looking forward for it, and started to manically laugh, and confused Scarecrow, who proceeded to inject Bruce with another dosage of his Fear Toxin.
This, however, allowed Batman to defeat his Joker side. With his fears gone, Bruce told Scarecrow how he was not afraid, who in turn started to threaten him with a loaded handgun. Jason Todd, who was hiding in the room, shot the gun out of Scarecrows hand, and then shot the lock of Bruce's gurney, who then injected Crane with his own Fear Toxin. This caused Crane to panic, as he saw demonic Bats everywhere he looked, and finally lost it as he saw a nightmarish Batman. Crane tried to run, but was immediately knocked out by Gordon. Batman remasked himself, told Gordon to look after his friends, and left the asylum with Crane.