Years later, Bruce began to use the caves to store his equipment secretly as the vigilante, Batman, and eventually transformed the cave itself into a base of operations for his continuing war on crime.
Before Arkham Origins Incident
Bruce investigated the den of bats and discovered a system of caverns that stretched beyond his 150 acre estate into most of Gotham City. Over time, Bruce and Alfred converted the caverns into his base of operations for his war on crime.
Bruce designed a training station, a workshop to design work on new gadgets, and a secret dock for the Batwing. The Batsuit was housed in a stand-alone container that rose from the dock station. The Batcomputer that can pick up all police radios all over Gotham, linked a experimental device that he borrowed and redesign from Wayne Enterprises called Detective Mode and a video surveillance system that was used to keep tabs on all of Gotham City. Bruce setup secret entrances and exits throughout cave that lead to Wayne Manor: one in the Study and the other in the Wine Cellar.
Arkham Origins Incident
The Batcave was accessible in Batman: Arkham Origins and worked as a hub to access Challenge Maps, Alternate Batsuits, and to talk to Alfred. It was first shown in the opening cutscene, with Bruce entering the cave and suiting up. He left via the Batwing to go to Blackgate Prison. From then on, Batman was free to come and go from the Batcave whenever they pleased.
Before the player could enter the GCPD and access the National Criminal Database, he returned to the Batcave and retrieved the Concussion Detonator, a new gadget from the workbench. Later that night he returned to retrieve the Glue Grenade. After arresting the Joker at the Royal Hotel, Batman returned to start his search for the gang leader known as Bane. Alfred suggested that he retire for the evening and enjoy some dinner. Batman disagreed and continued his investigation. He tuned into a police report giving him a lead and he then left for the GCPD Building. Bane had deduced Batman's identity, due to both Batman saying "You just ran out of time" and Bruce Wayne telling Vicki Vale the same phrase, plus flight maps that were tracked by Bane's followers that led straight to Wayne Manor. To crush Batman's spirit, Bane invaded the cave. Bane beat Alfed into submission and destroyed and burnt most of the equipment. Batman returned to find the cave destroyed and a beaten Alfred lying buried under rubble toward the bottom of the cave. After that, whenever Batman returned to the cave, it was still in the destroyed state, with several parts of it that were still smoking.
Cold, Cold Heart Incident
In the DLC, there was shown to be two working (post-Bane) entrances to the Batcave. The clock in the Study (although the player could not use this entrance because of all the guests in the room), and in the Wine Cellar as a fail safe. In the Batcave, some of the damage from Bane's attack was fixed by the time of New Year's Eve. But the workstation and Batmobile Prototype were still gone. It also appeared to be somewhat expanded with a new elevator that lead down into the cave by the Training Area from the Wine Cellar.
After The Cold, Cold Heart Incident
Following the incident with Mr Freeze and over the next few years, Bruce, Alfred and Lucius Fox extensively refitted and upgraded the Batcave. By the time of the Asylum Incident the cave was completely redesigned from its original appearance.
Arkham City Incident
Nightwing and Robin were both seen in the Batcave participating in a training simulation of TYGER Guards, who attempted to take over the Batcave, which was staged for them by Batman before the Arkham City Incident. After Bruce was captured and incarcerated in Arkham City, Hugo Strange's TYGER Guards attempted to take over both Wayne Manor and the Batcave to take advantage of Bruce being in Arkham City. Luckily, Nightwing, Robin, and Alfred stepped in to defend the Manor, took out the TYGER Guards, and managed to keep both Wayne Manor and the Batcave safe.
Arkham Knight Incident
In the "Father to Son" Trailer, Batman was seen meditating before he left to confront Two-Face. It appears that another entrance was created under a lake behind Wayne Manor. It was large enough for the Batmobile to fit through and led to the road.
In the "All Who Follow You" Trailer, Alfred is seen standing before the Batpod upon a platform of the Batcave, and during the events of Arkham Knight, when speaking to Alfred on the virtual screen of Batman's gauntlet, the Batcave can be seen as a backdrop to Alfred's person.
The Batcave did not appear in Arkham Knight, but in its place, there were 3 variants: The Clock Tower, Panessa Studios, and Bruce's Office at the top of Wayne Tower. It was unknown if the Batcave was destroyed during The Knightfall Protocol, although it was possible that Batman and Alfred had somehow made it into the Batcave right before Wayne Manor was destroyed if the Batcave wasn't destroyed. If that was true, then it was more than likely that Nightmare Batman was truly Bruce.
- The Batcave Challenge Map was featured in the Challenge Map DLC Pack for Batman: Arkham City.
- The Batcomputer mentioned how many TYGER Guards remained as well as those that were taken out.
- Near the Batwing, on the ground beside the grate, was the Grapnel Boost and several of the containment pods that housed the Batsuit at the beginning of the game.
- There was a statue construct of Batman in the hallway to the right of the T-Rex in the Batcave Challenge Map.
- There was a reference to Jason Todd, the second Robin, in The Batcave Challenge Map. The Batmobile was without its tires, which referred to the first encounter between Jason and Batman, when Jason was trying to steal the tires from the Batmobile, and in Arkham Unhinged, there was a glimpse of Jason's Robin uniform on display in the cave as it was a memorial to him when he was killed by the Joker.
- On one of the monitors in the Batcave. there was a video that showed the Church and Medical Center in Arkham City. The other one was from Arkham Asylum.