The Sun Stone is an illustrious artifact with the ability to store elemental, magical power. It aided in the rise of Zeal and has been written into legends across the eras. It was the foremost source of the elemental energy and magic harnessed by the citizens and sorcerers of Zeal. It was also used to create elemental weapons and armor, including the Black Mail, Blue Mail, Red Mail, White Mail, Swallow, and other artifacts that were spread across the land in the Fall of Zeal. It is apparent that the people of Zeal once owed their well-being to the planet and her natural gifts; however, with the advent of the Mammon Machine, elemental energy usage was forbidden and the items created with it were sealed up in the North Palace. After 65000000 years, the Sun Stone was also probably growing dim at this time, leading to such statements as "we do not need the energy of this tired, old planet." Only Melchior retained skill in forging elemental items during this transition to Lavos's power, and in due time, the Sun Stone was sealed up in the Sun Palace. After Zeal fell, the Sun Palace lay submerged for 14300 years until it was uncovered by the heroes of time in 2300 A.D. In this time, the Sun Stone, now a dormant Moon Stone, was taken (but only after a fight with the Son of Sun, probably an elemental defense mechanism emplaced by Zeal).
The Moon Stone was left in the Sun Keep in 65000000 B.C., where, after being lost to the Porre Mayor and subsequently recovered, it regained its former luster and was used by the party to create the Sun Shades (by Taban), WonderShot (by Lucca), and later, the Rainbow (by Melchior), fulfilling ancient prophecies that combining the Sun Stone with the power of the Rainbow Shell would lead to incredible weapons and items. It is unknown what became of the Sun Stone after this event; it was most likely kept in Lucca's possession.
The burning of Lucca's Orphanage -- possibly housing the Sun Stone in 1015 A.D. -- suggests dark circumstances if it were recovered by Porre forces or even Lynx. However, Chrono Cross does not elaborate on this possibility.