He attended the National Gallery along with Kate Stewart and Osgood after the Under-Gallery was breached, and was in the party that welcomed the recently summoned 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 to the Black Archive.
He was 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.
He confronted the Zygon duplicates of himself, Kate Stewart and Osgood in the Black Archive, and sealed the doors on Kate's orders. McGillop stood by Kate's decision to arm a nuclear warhead with the power to obliterate London. He 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 (which he had previously moved to the Black Archive), who then proceeded to wipe the memories of the Zygon duplicates, and the human originals in the Black Archive. He negotiated the human-Zygon peace treaty. (TV: The Day of the Doctor)