Scarecrow's Lair

Scarecrow maintained a hidden lair in Arkham Asylum under an elevator in the Intensive Treatment Center.

Arkham Asylum Incident
Scarecrow used that lair to monitor Batman and used mushrooms to make his Fear Gas. When Harley Quinn dropped the elevator on Batman, you could visit that lair to solve one of the Riddler's Riddles.

Inside, Scarecrow had blueprints of Arkham Asylum, computers and security monitors, photographs of Batman, and canisters of Fear Gas.

Arkham City Incident
Scarecrow had a new lair in the Industrial District: a boat near Warehouse 5B in the Falcone Shipping Yard. The access code to the hatch was the hardest Cryptographic Sequence combination in Arkham City: "City of Terror" (Level 5). Inside Scarecrow's lair were glass tanks of live bugs. Some of the tanks were smashed, and the insects were crawling in the ship. A Joker Henchmen was sitting in a chair at the end of the barge, and was captive for Scarecrow's tests. When zoomed in on, the henchman panicked and collapsed back into the chair. On the wall to the henchman's left was an invoice that detailed shipments from Falcone Shipping to Scarecrow, and mentioned The Broker.

Arkham Knight Incident
It was unknown where exactly Scarecrow had his base, as he had multiple smaller locations that he used during the Main Story. First, Scarecrow used a Penthouse in Chinatown, where he kept Poison Ivy prisoner. Then Scarecrow had access to a small warehouse on Miagani Island, where he had stashed the props used during the game, such as the demonic masks. Scarecrow was finally confronted at the abandoned Arkham Asylum, where he also had had a meeting prior to the game's events. He might also have used the Militia Headquarters, in the abandoned shopping mall on Founder's island.