Underneath Arkham Asylum consisted of caverns, an old sewer that emptied into the Gotham River, an unused Pump Station, and Killer Croc's Lair. The Caves also included a top-secret Batcave that Batman had built on Arkham Island.
Arkham Asylum Incident
When the Joker began to take control of Arkham Island, the Arkham security guards were posted around the entrance to the Caves to the Pump Station, which had been closed by Warden Sharp years earlier on the grounds that it was a security threat. When Arkham East was overrun by the Joker's Henchmen, they killed the guards, infiltrated the Caves, and entered and secured the Old Sewer.
The escaped Blackgate Prisoners killed an Arkham orderly near the entrance to Killer Croc's Lair and remained on guard there under the Joker's orders. Batman, meanwhile, had accessed the Batcave near the Old Sewer. The Batcave included a Batcomputer, which Batman used to do research on Dr. Penelope Young's formula for Titan. Batman then assembled the Batclaw by using spare gadgets among the equipment stored in the Batcave. He proceeded to the Old Sewer, and defeated the prisoners. The Joker was talking to one of his henchmen who was positioned in the Old Sewer via walkie-talkie, but when he lost contact, Joker contemplated aloud if the henchman had been cut off by Killer Croc or Batman.
However, Croc was still in his lair, and he spotted Batman as the Dark Knight passed a bolted metal door that lead into his lair. Croc smashed against the door and cracked the window glass, but was unable to reach Batman. From the Old Sewer, Batman entered the Main Sewer Junction, which he found was filled with decrepit columns, archways, and platforms. Batman also found he couldn't use his Grapnel Gun in very many places there as most of the surfaces were not strong enough to support his weight. Batman then escaped back to the island surface by using the Surface Access Corridor that lead into an abandoned building in Arkham North.
Shortly after the Joker had perfected the Titan Formula, one of his Titan Henchmen wandered into Croc's Lair, which proved to be a fatal mistake. Poison Ivy's mutated plants begun to destroy the asylum, and the Old Sewer and the Pump Station were increasingly damaged by the Titan-fueled plants. Batman, following the villainous Scarecrow through Secure Transit at the Intensive Treatment Center, found an alternate route into the Caves through the Control Room Access in the lower level of Secure Transit. Batman entered, and found the remains of Joker's unfortunate Titan subject. He also found Scarecrow holding a bag of his Fear Toxin over the water and threatened to flood the Gotham River with it.
However, Croc leaped from the water, captured Scarecrow, and intended to kill him. Batman activated Croc's shock collar by throwing a Batarang at it, which caused Croc and Scarecrow to disappear under the water. Batman then entered Croc's actual lair that proved to be a labyrinth of tunnels that were not mapped. Batman set a Batscanner that was tuned to lead him to the rare plant spores that were needed to create an antidote for the Titan Formula. After he found the spores, Batman reset the Batscanner so it could lead him back to the the entrance of Croc's Lair. Croc began leaping out of the water and chased Batman from under the floating wooden platforms that covered his lair. Batman made his way back to the entrance via the Batscanner. Croc pursued Batman all the way to the mouth of his lair, and Batman found that iron bars had mysteriously blocked his exit. But Batman detonated his Explosive Gel on the breakable stone floor under Croc as he charged, and dropped him down further into the Caves. Batman slipped under the bars, and re-entered the Old Sewer.
The Joker dispatched a group of Blackgate Prisoners to find the Batcave, but Batman defeated them in the Old Sewer. Upon reaching the Main Sewer Junction, Batman found the entire water flow was polluted by Titan waste. The Joker was planning to flood the Gotham River with Titan, and cause chaos. Batman invaded the Pump Control Room to shut off the Titan flood. He defeated several of the Joker's men in the Pressure Control Junction. Batman reached the Pump Room, and shut off the Titan pumps after he faced seven more Blackgate Prisoners.
As Batman backtracked to the Pressure Control Junction in the Caves, and once he entered the center of the junction, the Dark Knight was locked in by electronic barriers and forced to fight his way through hordes of Joker's Henchmen and one Titan Henchman. After he wrecked the Pressure Control Junction and defeated the henchmen, Batman destroyed the elevator that lead from Arkham West and exited the Caves. The Caves, mainly the sewer parts, were heavily damaged and shaken by more earthquakes that were caused by Poison Ivy's Plants, and toxic plant pods began to appear in the Old Sewer and the Main Sewer Junction. The Caves were reclaimed by the GCPD as they took over Arkham Island after the Joker's defeat.