The Ancient Minister is the primary antagonist for the majority of the Subspace Emissary. He appears to be the leader of the Subspace Army and controls the R.O.B. Squad and their deployments of Subspace Bombs.
He is considered to be a tragic villain (an antagonist who does not truly intend to be a villain), as he truthfully regretted his actions of bringing the World of Trophies into Subspace under the orders of Tabuu and he was coerced into doing so.
At the end he was betrayed by Master Hand's henchman Ganondorf to die in the explosion of the Isle of the Ancients, but he resorted to his true R.O.B. form and joined the heroes in the quest to defeat Tabuu.