McGillop attended the National Gallery along with Kate Stewart and Osgood after the Under Gallery was breached, and was in the party that welcomed the Eleventh Doctor and Clara Oswald. As the rest of the party moved on, he received a telephone call from a future version of the Eleventh Doctor who instructed him to move the painting Gallifrey Falls No More to the Black Archive.
He was later called to the Under Gallery by Osgood to help analyse the stone dust that covered the floor of the statue room. He came face to face with an alien race, the Zygons, and was duplicated by them. (TV: The Day of the Doctor) He was later freed from captivity by Osgood. (PROSE: The Day of the Doctor)
McGillop confronted the Zygon duplicates of himself, Kate and Osgood in the Black Archive, and sealed the doors on Kate's orders. He stood by Kate's decision to arm a nuclear warhead with the power to obliterate London, and cut the Tenth Doctor, War Doctor and Eleventh Doctor from communicating with the Black Archive by disabling the space-time telegraph.
He became a victim of his own actions, as the Doctors then emerged from the stasis cube in Gallifrey Falls No More, and then proceeded to wipe the memories of the Zygon duplicates, and the human originals in the Black Archive. Not knowing which side he was in favour of, McGillop helped negotiate the human-Zygon peace treaty with Kate and their Zygon counterparts. (TV: The Day of the Doctor)