Isle of Ancients
Before Tabuu invaded the Isle of Ancients, the Ancient Minister was known as the Master Robot. During Tabuu's invasion, he enslaved the R.O.B.s to help him create Subspace Bombs and other weapons for the Subspace Army. Not wanting to lose the R.O.B.s to Tabuu, the Master Robot reluctantly joins Tabuu's side and was renamed Ancient Minister.
Super Smash Bros. Brawl
In Super Smash Bros. Brawl, during the events of The Subspace Emissary, Ganondorf takes control of the R.O.B.s on the Isle of Ancients, and he forces them to detonate several Subspace Bombs at once. He does this to transport a Subspace Gunship through to the World of Trophies.
After the defeat of Tabuu, a shining "X" appears in the sky where the Isle of Ancients was. It did not return to the world because of all the Subspace Bombs that detonated at once. The shining "X" also appears in the opening sequence for the main game.