The 77-minute episode shows the last day of the Time War, in which the War Doctor (John Hurt) chooses to kill both Daleks and his own race of Time Lords to end the destructive conflict, paralleling this with a present-day choice by paramilitary organisation UNIT to destroy London rather than allow an alien invasion.Revising the back story, the Doctor succumbs to Clara Oswald's plea to change his mind; and instead, at the last instant of the Time War, he hides his war-torn home planet in time, rather than destroy it.It questions whether mass killing is the best option for ending the Time War and prescribes the Doctor's punishment if he does so — he will survive while the rest of his race dies.The Moment offers to show the Doctor what this will turn him into and opens a fissure linking him to the Tenth and Eleventh Doctors.The "Fall of Arcadia" becomes the central battle of the Time War around which "The Day of the Doctor" is centred.The Eleventh Doctor and Clara Oswald aid the military organisation UNIT, headed by Kate Stewart, in investigating a mystery at the Undergallery, a secret vault housed at the National Gallery.The Doctor is resurrected temporarily by the Sisterhood of Karn (who control a secret Elixir of Life in the 1976 serial The Brain of Morbius).
She and the Doctor die as the ship crashes on Karn.
Meanwhile, within UNIT's Black Archive, Clara learns that the Zygons from Elizabethan England have entered the three-dimensional paintings in the Undergallery and have emerged in 2013, taking the forms of UNIT members so that they could utilise UNIT's weapons and technology.
While the three Doctors are in their cell, The Moment encourages the War Doctor to ask them the questions he needs answered before he decides whether to destroy Gallifrey.
The War Doctor, now convinced that detonating the Moment will save many more lives in the longer term, is returned to his time by the Moment.
The other two Doctors follow him in their TARDISes with the intention of helping him so as to share his burden.