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It is not explained in either "The Day of the Doctor" or "The End of Time" why this particular event was retained in his memory while others weren't, however some other multi-Doctor adventures, such as "Time Crash", suggest that there is some small level of memory retention after the end of an encounter with past incarnations of ones self, such as in "Time Crash" when the Tenth Doctor remembers the method he previously used to stop the paradox caused by his meeting with his fifth incarnation from creating a hole in space-time the size of Belgium. The Doctor's marriage to Queen Elizabeth I must be one such fact which slips through the memory wipe.