Mulligan was a pirate on the Fancy in the 17th century. Mulligan started a mutiny with the boatswain against Captain Avery. However, he cut his hand, giving him the black spot. He was then taken by the Siren to her ship, and later joined the rest of the crew when they took the ship for themselves. (TV: The Curse of the Black Spot)
Some time later, the Doctor recruited Avery to help him with an attack on the asteroid of Demon's Run to rescue Amy Pond. Mulligan and the crew boarded the ship of Madame Kovarian during the attack and subdued its crew, preventing her escape. (TV: A Good Man Goes to War)