After becoming a father made him want to be a better man, Thomas Wayne began asking hard questions about Wayne Enterprises, using this space as his secret workplace. He later left a letter to his son, Bruce in the case of his death, in the lair.
Alfred smashed up a computer containing information on Wayne Enterprises, in an attempt to try and protect Bruce. However, he later hired Lucius Fox to fix it when Bruce was determined to find out the truth. Lucius succeeded in restoring the computer's functions. 
During No Man's Land, the Wayne Manor became abandoned since Alfred and Bruce decided to stay on the Gotham island. However, Jeremiah Valeska and his assistant Ecco recruited the Soothsayers and started to dig a tunnel underneath the Gotham River to reach the secret cave underneath Wayne Manor on the mainland. When Ecco and her goons finally managed to break through, the sound of bat wings could be heard from inside the lair. Ecco immediately woke up Jeremiah and the two villains then proceeded to walk through the secret passageway and inside the library room of Wayne Manor.
- "Rise of the Villains: Damned If You Do..."
- "Rise of the Villains: Knock, Knock"
- "Rise of the Villains: By Fire"
- "Wrath of the Villains: A Dead Man Feels No Cold"
- "Wrath of the Villains: This Ball of Mud and Meanness"
- "Wrath of the Villains: Pinewood"
- The code to unlock the door to the lair was "BRUCE", although Alfred and his ward blew the door open.
- In numbers, the code would then be "27833."
- The lair acts as a precursor to the Batcave, a place that Batman uses as his hideout in much of the Batman related media and where he also keeps his costumes and gadgets. This is further supported when bats could be heard flapping around at the end of "All Happy Families Are Alike".
- ↑ 1.0 1.1 Heller, Bruno (writer) & Cannon, Danny (director) (September 21, 2015). "Rise of the Villains: Damned If You Do...". Gotham. Season 2. Episode 1. FOX.
- ↑ Woodruff, Ken (writer) & Bailey, Rob (director) (September 28, 2015). "Rise of the Villains: Knock, Knock". Gotham. Season 2. Episode 2. FOX.
- ↑ Heller, Bruno (writer) & Hunter, Jeffrey (director) (November 30, 2015). "Rise of the Villains: Worse Than A Crime". Gotham. Season 2. Episode 11. FOX.
- ↑ Woodruff, Ken (writer) & Copus, Nick (director) (February 29, 2016). "Wrath of the Villains: Mr. Freeze". Gotham. Season 2. Episode 12. FOX.
- ↑ Sosa, Iturri (writer) & Tonderai, Mark (director) (January 31, 2019) "Pena Dura" Gotham. Season 5. Episode 5.