The Catacombs were originally part of larger excavations undertaken by the Romans to remove valuable deposits of gypsum and limestone from the area. The Catacombs date back to 1786 when bones were removed from the grossly overcrowded Cemetery of Innocents to be stored in the quarries of Mont-Rouge. Since that time, innumerable additional burials have resulted in the vast ossuary.
During World War II, the Catacombs were used as bunkers.
In the early 2050s, the catacombs are used by Silhouette to resist the martial law imposed in Paris by Majestic 12 soldiers and bots. An MJ12 agent Mari Hela is in charge of the operation to flush out the remaining members of Silhouette, led by Chad Dumier, that had not already been killed or surrendered above ground.
In 2052, JC Denton enters the catacombs to find Chad Dumier in the hope of finding Nicolette DuClare and ultimately Morgan Everett. To acquire Chad Dumier's cooperation, JC rescues two members of Silhouette who are being held hostage in bunker #3, and returns them to Chad in bunker #1.