The Rune Stone is magical stone that is linked to Queen Maeve from a deal with Mider. It is the source of Maeve's power, and link to the deep, dark pits. It is capable of teleportation, conjugation of creatures and various spells and illusions.
At the end of the series, Queen Maeve uses all of its power at once to transform herself into a Naga-esque creature.
When Maeve was defeated, the Rune Stone vanished, leaving her without a way to use her magical powers.