The building was constructed and owned by Wayne Enterprises and as most of the buildings owned by that company, the Clock Tower was fortified against earthquakes. The Tower was used since the beginning as Barbara Gordon's living place and base of operations. Barbara installed many computers that allowed her to begin her work as Oracle. In this job, Barbara was the main source of help for Batman and the Justice League providing information that they needed on their respective missions. The Clock Tower was also used as meeting point for the Bat-Family during No Man's Land and also as a base of operations for the Birds of Prey.
Barbara also installed a maximum security system in the Tower to protect herself as well as the many records and files she had saved over the time on her duty as Oracle. The security system consisted of traps like lasers, trap doors, electrified fences, flashing lights, sliding staircases and more. This security measures proved useful during No Man's Land, when the Tower was targeted twice: one time by Black Mask and the second time by William Pettit.
The Clock Tower was destroyed at the end of the Gang War that shattered Gotham. Black Mask learned about the place from Stephanie Brown, whom he tortured to confess some of Batman's secrets. Black Mask mistook Stephanie's confession and then he told the people of Gotham that the Clock Tower was in fact the Batcave and that he would destroy it as the ultimate act of superiority against Batman and as a way to establish his crime empire. Batman and Black Mask fought in the main chamber with Barbara as witness. They were killing each other and in order to make them stop, Barbara activated the auto-destruction sequence and locked all the ways outside. She did so in order to stop Batman from fighting Black Mask and save her instead, as she wasn't able to get out. Batman managed to save Barbara just when the whole building collapsed from the explosions caused by the auto-destruction sequence.