The Ruby and Sapphire first appeared in It All Ends Now VIII. After the Red and Blue Orbs had been destroyed by Ruby's Celebi, their shattered remains fell to the ground and were found by Giovanni, who revealed that the formed gemstones were actually the Orbs' true forms.
The gemstones played a notable role during Team Rocket's plan in this arc. In Not Exactly Normal, Sird was revealed to have used the gems on Deoxys after it had defeated Red in a battle, allowing it to stabilize its Normal Forme, as well as access its Speed Forme. It was later revealed that the gemstones were able to replicate the climate of Hoenn in the Kanto region, giving Deoxys full access to all four of its Formes in Kanto and the Sevii Islands.
In Double Down Deoxys, Bill and Celio raided the Rocket Warehouse on Five Island, where the gemstones had been stationed in an amplifier, which had spreaded their influence to cover the entire Kanto region and Sevii Islands. Once Bill removed the gemstones from the amplifier, Deoxys lost its access to its Normal and Speed Formes in the Kanto region, allowing Mewtwo to defeat it aboard the Team Rocket airship. Bill subsequently took the gemstones with him to the Sea Cottage.
In PS607, the gemstones were revealed to have started regenerating back into their states as the Orbs they had been before. The reforming Orbs were stolen by Archie and Maxie, who headed back to Hoenn with them. By the time they reached Hoenn, the Orbs had finished reforming.