They are first heard of when Cyrus asks for the rare blue Keystone from the Ruins. The Red Keystone can be found on the planet of Ziba in the possession of Professor Kate, who is researching the Keystones and the Ruins of Nessa. The Green Keystone can be found in the Kollin Museum, as the main artifact. Later, to get the Blue Keystone from Cyrus, he asks for a Diamond mineral in return.
The Keystones are used to power the Ancient Starship, which is discovered by Professor Kate to be part of, if not the whole of, the Ancient Ruins.
They are most likely lost on Nox when the ship crashed and was destroyed.