The Underground Sanctuary is the newest and main branch of the Sanctuary Network, hidden at a secret location beneath the surface of the Earth. It is the largest and most modern Sanctuary ever built, believed to hold room for all Abnormals in the world.
After she travelled back through time, Dr. Helen Magnus realized that her concept for the Network would not work into the 21st century, so she made preparations to change its nature when she resurfaced from her self-imposed exile in 2011.
When the Old City Sanctuary was destroyed, the new underground headquarters was already up and running. Magnus revealed its existence to Will Zimmerman a few days later, noting there was a lot of work to do.
Notes and References Edit
Fourth season deleted scenes show Tesla accusing Magnus of hiding secrets, and that in the early 20th century she (or rather her hidden self) had him develop TNT devices to try and find a nonexistant underground cave dwelling abnormal shark in Peru/Bolivia - an area that he now knows to provide direct access to Hollow Earth. This could be the real location of the underground sanctuary, plugged into the original Praxian transport system.
Given that the Underground Sanctuary obviously uses variations of Praxian technology, it is widely speculated that Magnus collaborated with the Praxians during her second trip through the 20th century, possibly even saving some of the city's population before Worth destroyed it.