In the depths of the Red Cathedral in Mechanicsburg is the mysterious artifact known initially as the Monolith. Under normal circumstances, this device allows for instantaneous transport between it and a similar mechanism/gateway at a remote location; one such connection is located in The Refuge of Storms, and it is eventually confirmed that other such connections exist elsewhere, albeit mostly in a far less functional state. (See below.) It's been pretty well established that the Monolith is much older than the Cathedral that now surrounds it; it is unknown if said Cathedral was intentionally built on top of it.
Well in advance of our heroine Agatha Heterodyne coming into power over Mechanicsburg, at least one faction of the organization called The Knights of Jove was aware of the existence of the Monolith and knew how to operate it, to the point of being able to construct the Refuge connection; how much further this knowledge has currently (re-)spread is also unknown. During the Siege of Mechanicsburg, two members of The Storm King Conspiracy, The Abbess of the Red Cathedral and Martellus von Blitzengaard, attempt to take a kidnapped Agatha through the Monolith gate; following a jumbled melee in the Monolith chamber, Agatha, Tweedle, Violetta, Krosp and a solitary Wasp-Eater are the ones who make the jump.
Because they all do this at the exact moment which Klaus Wulfenbach activates his time-freezing "Take Five" device, the trip, still subjectively instantaneous for the travelers, takes two and a half years as far as the rest of the world is concerned. This event is referred to by Girl Genius fans as the Timeskip. The effort of retrieving/accepting eventual arrival of this group the The Refuge gate to explode; the status of the Mechanicsburg Monolith is, yes, unknown.
A Wider Connection
Upon (eventually) being told how Agatha escaped Mechanicsburg, Zeetha immediately makes a to a piece of Skifander lore, "Queen Luheia's Mirror", a magic gate that the first Skifander inhabitants evidently used to originally travel to their far-off home. Unlike the Monolith, the Skifander Mirror has long been dormant. Later still, Queen Albia of England that she too is in possession of a non-functional Mirror, and reveals there was once a network of the devices by which she communicated with her fellow Queens. There has been no indication as yet which Queen, if any, originally controlled the Mechanicsburg Monolith. However, that Mechanicsburg was originally built around the spring that became the source of the Dyne, and that spring was considered "sacred to the local battle goddess", which may be a reference to a Queen.