The Botanical Gardens of Arkham Asylum provide fresh greenery as possible rehabilitation for the institution's inmates. It includes a Statue Corridor, an Aviary, and even a top secret Titan Production Facility used by Dr. Penelope Young.
With Arkham East the only part of Arkham Island under control during the early stages of the Joker's takeover of Arkham Island, security guards were posted around and within the Botanical Gardens.
While several guards patrolled the outside, one guard was posted at the Glasshouse Entrance, and two others at the entryway to the inner Botanical Gardens. Shortly after armed convicts stormed Arkham East, the gardens fell to them as well. Victor Zsasz raided the Glasshouse Entrance and killed the security guards, arranging them in a lifelike pose around a bench. The Joker's men then entered the inner Gardens, meeting little resistance.
After Batman defeated them, he continued back through the Abandoned Corridor, and to the other side of the Flooded Corridor, where two convicts had turned the power back on, attempting to trap Batman on the other side of the Flooded Corridor by re-electrifying the water. Batman grappled across the water using his Line Launcher and defeated the Blackgate prisoners. He returned to the Glasshouse entrance after defeating more of the Joker's men in the Botanical Glasshouse. Here, the Joker broadcast triumphantly over Arkham's intercom that he had supplied Poison Ivy with Titan.
The plants of the Botanical Gardens mutated and overran the Botanical Gardens, mainly destroying the Garden's facilities. Batman found his exit blocked by the mutant plants, but escaped using an alternate route through the flooring. The remains of the Botanical Gardens soon became filled with Titan Pods which could spit toxic gas orbs at any movement. Batman returned to the Gardens to battle Ivy, who cleared her vegetation out of the way for him to proceed. She allowed him to re-enter the Flooded Corridor, where she unleashed two security guards under her control to attack and weaken Batman. After being forced to defeat the zombified guards, Batman was lured further into the Gardens by the mutated plants.
He found Ivy in the Elizabeth Arkham Gardens, where she bounds with a titan plant, controlling the massive plant from inside its mouth behind a shell. She powered toxic vines to grow out of the ground and sent Arkham security guards infected by her mind-controlling spores after Batman, who finally knocked down all the guards and fought off the vines, detonating explosive gel on the mutated plant and defeating Ivy. The ruined Botanical Gardens were reclaimed by the GCPD as they recaptured Arkham Island.