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 the Omega Ruby & Alpha Sapphire chapter, 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 of they reached Hoenn, the Orbs had finished reforming.