The Ancient Minister.
The Ancient Minister seems to be the leader towards the beginning of the Subspace Emissary. He's in quite a few cut scenes in the Subspace Emissary, often seen dropping bombs to bring the world in to the world into the darkness. He is almost taken down by Mario, Pit, and several others. As the story progresses it begins to seem like he doesn't like what is happening, and is remorseful about the sacrifice the R.O.B's have to make to detonate a subspace bomb. When a group of heroes finally catch up to him, he is reluctant to fight. At that moment however a hologram of Ganondorf appears and orders the R.O.B's to begin detonating all of the subspace bombs in the room. The Ancient Minister tries to stop them, however the R.O.B's attack attacking and his costume burns off revealing he is in fact R.O.B., he then joins up with the heroes and helps them escape.
On the Smash Bros Dojo the director of the game, Sakurai, give a more detailed explanation of some of the parts of Subspace Emissary that were a little hard to understand. There it was revealed that R.O.B. had been the leader of a of a race of highly advanced but peaceful robots who lived on an island in the sky. Tabuu and his subspace army attacked and took the island hostage, so R.O.B. agreed to let them use the island as an offensive base. R.O.B. was put in charge of the base, however he was ashamed of having betrayed his people so he disguised himself as the Ancient Minister.