Sun Stone (Origin of)
What is the origin of the Sun Stone and its history?
Keep in mind while reading these theories that the Sun Stone was apparently powered up long before 65000000 B.C., as it was found and used extensively by Zeal in 12000 B.C., while the time travelers cannot use it until exactly 65002300 years of charging have passed. That it is absent from the Sun Keep also suggests that it was powered up long before prehistory, and simply wasn't found until the founding fathers of Zeal located it.
See Sun Keep (Origin of), Planetary / Magical Connection. The Sun Stone, along with the Sun Keep, could have been a natural formation akin to Power Spots. By extension, the Sun Stone could also be a natural formation; it would have been charged up before 65000000 B.C. and then removed from the Sun Keep somehow, where it would have lay dormant for millions of years until found by Zeal and utilized there. Once again, this does not account for the torches in the Sun Keep, but those may have been placed there by the Iokans or Reptites prior to Crono's visiting the area in prehistory. Two other problems plague this theory. Mainly, the formation of a unique "battery" and its lucky placement in a unique "charger" is almost ludicrously coincidental. Secondly, the material the Sun Stone is made out of is not observed anywhere else in the game, suggesting it is completely unique (perhaps engineered by a sentient species).
Complete Mystery / Plot Oversight
Some civilization of group of beings were using the Sun Stone prior to 65000000 B.C. Since nothing corroborates such a claim except a quote by Lucca stating that solar energy was used before Lavos, the Sun Stone was perhaps an oversight by the developers, who didn't realize that by having Crono and his team leave it in the Sun Keep, they precluded the ability for it to be left in the Sun Keep by anyone else to be found by Zeal before 12000 B.C.
Temporal Displacement Mystery
The Sun Stone was created as a way of harnessing the planet's elemental energy by either the Reptites or others, and somehow was displaced in time. This theory is pure, unbridled speculation, sadly.
From: Theory (Objects)