As stated by Velziran, the portals—and their exit points in corresponding settlements—are powered by energetic currents called leylines. These currents are naturally-occurring, and exist within the land itself. A set of Waygates in the World Above used to be accessible to Mages, but have since been sealed by the Vostinian Empire.
The party's Waystone is a non-consumable item that can be activated from within the Items menu (provided that the group is not in combat or a cutscene). Confirming the use of the Waystone will transport the player to an area containing all of the Storynth's Waygates. The number of portals accessible to the group depends on their progress through the main storyline.
After using one of the portals in the Waygates, the party will generally appear on the Waygate marker in the appropriate location.
A different variety of Waystone for use by Fiendish nobility. While the fundamental function is identical to a typical Waystone, it also appears possible to travel to locations without a traditional Waygate marker. Only two of these Waystones are known to exist during the events of Storynth.