The injectors have drills, which they use to dig deep underground. they then place a gem. (watch pearls description in Keeping it Together.) so, Gem drill. in On The Run, Amethyst says that they are all busted by now. maybe exept one. one gets turned on and creates a gem?
Theory: The gems find an injector working, so pearl and garnet form sardonyx to drill down. the gems travel down to the center of the earth to retrieve and bubble the new gem before it "hatches".