The Commander of the Ark was the leader of the Guardians travelling on the Ark in Earth's far future in order to find a new home for all species of Earth, whose sun was going to destroy the planet. This commander was the leader at the time of the First Doctor's first visit to the Ark. He was the father of Mellium.
When the Doctor visited the Ark the first time, the Commander welcomed him and his companions. However, the Commander, along with several others, caught Dodo's cold, to which they had no resistance as the cold was eradicated long ago. The Doctor and his companions were put on trial by Zentos, but the Commander, from his sickbed, ordered that the Doctor be allowed to find a cure. When the Doctor found the cure, he tested it successfully on Steven before curing the Commander and the rest of his people that were infected. (TV: The Ark)