The Munition Tunnels are an underground network of tunnels, built during the time of the American Revolution. They connect the Westchester County Police Station, The Archives, and the Masonic Cell. Ichabod Crane is very familiar with the Tunnels' structure.
The Headless Horseman chased Crane and Abbie through the Tunnels, littered with fake skulls, only to be weakened and captured in the Masonic Cell with ultraviolet light. Undead Andy Brooks also had a small dwelling in the Tunnels, where he was later put into a cocoon during his metamorphosis.
The Witnesses found the Kindred's body parts hidden in the Tunnels. In the early episodes of Season 2, Crane had no choice but to sneak through the Tunnels to get to the Archives, because Sheriff Reyes considered him to be an unauthorized person.