Aliases of the Doctor

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Throughout his travels in time and space, the Doctor took and was called by a number of different aliases, titles and names. Some were fleeting. Others, for example John Smith, were used by almost all of his incarnations. The Doctor told few individuals his real name, causing others to call him the Doctor.

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Names given by others

A list of names other individuals have called the Doctor throughout his travels.

The Doctor: While some accounts contradict this, Barbara Wright and Ian Chesterton may have accidentally given him this title, after being informed that his alias of "Doctor Foreman" was not his real name and given no other name to call him (TV: An Unearthly Child). The Doctor did not protest and, by the end of the sixties, starts introducing himself by this name. ^{[source needed]}
Doctor Who: The name Doctor Who was applied to the Doctor, intentionally or unintentionally, on many occasions. The computer WOTAN once referred to the Doctor as Doctor Who, for reasons which have never been explained. (TV: The War Machines) Clive Finch also used this name when referring to the Ninth Doctor on his website Who is Doctor Who?. (TV: Rose) K9 was heard on occasion making playful remarks related to the Who name. (TV: A Girl's Best Friend, TV: Invasion of the Bane) It is unclear whether the Doctor himself ever actually used the name, although his third incarnation drove an automobile with the licence number "WHO 1" (TV: Doctor Who and the Silurians, et al) and not long before his regeneration was seen driving a futuristic vehicle that possibly apocryphal sources suggest may have been called the Whomobile. (TV: Invasion of the Dinosaurs) The Doctor wrote a series of children's books during his time with UNIT which were mistakenly published under this name. (AUDIO: The Kingmaker)

The name was often unintentionally invoked when characters wished to learn who the Doctor was and what his name was: "Doctor? Doctor who?" Often this is done for comic effect; see The "Doctor Who?" running joke.

First Doctor

Doctor Foreman: Used by Ian Chesterton and Barbara Wright, who assumed he shared Susan's surname. (TV: An Unearthly Child).
The Traveller from Beyond Time: The epiphet given to the Doctor by the Elders. (TV: The Savages)

Second Doctor

Ka Faraq Gatri (Destroyer of Worlds): As early as his second incarnation, the Doctor knew that the Daleks had given him this epiphet, and the Daleks used it prior to the destruction of Skaro. (COMIC: Bringer of Darkness)
Doctor Galloway: Edward Waterfield made up this name for the Second Doctor when arranging to meet him. (TV: The Evil of the Daleks)

Third Doctor

Quiquaequod: Miss Hawthorne referred to the Doctor as "the great wizard Quiquaequod" while attempting to bluff the villagers of Devil's End into releasing him. (TV: The Dæmons)
Prisoner 177781: The Doctor was recorded by this designation when he was briefly arrested by the British Army alongside Sarah Jane Smith, who was recorded as Prisoner 177782. (TV: Invasion of the Dinosaurs)

Fourth Doctor

The Evil One: The Sevateem tribe referred to the Doctor as the Evil One. The supercomputer they worshipped had two personalities, one of which was based on the Fourth Doctor. (TV: The Face of Evil)
The Watcher: To refer to a projection of the Doctor partway between his fourth and fifth incarnations, before they realised his true identity. The only individual heard to utter it was Adric. (TV: Logopolis)

Sixth Doctor

Old One: Given by Balazar while investigating Ravalox. (TV: The Mysterious Planet)
The Sandman: The Sixth Doctor's actions in the past of the Galyari led to his entering their race memory as a legendary monster called the Sandman. (AUDIO: The Sandman)
The Dark One / He Whose Name Dare Not Be Mentioned: Names given to the Sixth Doctor/the Valeyard in the legends of the Great Kingdom, an unstable alternate version of London created by the botched summoning of Saraquazel. (PROSE: Millennial Rites)

Seventh Doctor

Commander John Ballard: The Doctor was mistaken for the new commander of Dark Space 8 after he and Melanie Bush were teleported aboard the station following the destruction of Ballard's shuttle. (AUDIO: Bang-Bang-A-Boom!)
The Oncoming Storm: was also the epithet given to him by the Draconians, ("Karshtakavaar" in Draconian) who were generally the Doctor's allies, to indicate the traumatic events which so often accompanied his arrival. (PROSE: Love and War)
Time's Champion: A title given to the Doctor for his service to Time during his seventh incarnation. (PROSE: Love and War)
Ka Faraq Gatri (other Dalek names): The Daleks referred to the Doctor as the Ka Faraq Gatri, which may mean Bringer of Darkness and/or Destroyer of Worlds. By implication, the epiphet Destroyer of Worlds referred to the Doctor's destruction of the Dalek home planet Skaro in his seventh incarnation, an act for which he would feel some remorse. (TV: Remembrance of the Daleks, PROSE: Timewyrm: Revelation, AUDIO: The One Doctor)
Snail or Wormhole: Given to him by his cousins of the House of Lungbarrow, because, unlike Loomed Gallifreyans, he had a bellybutton. (PROSE: Lungbarrow)
Merlin: The Doctor was mistaken by the people from an alternate universe which inspired the Arthurian legend to be Merlin. It is intimated that a future or alternate version of the Doctor may in fact be this Merlin. (TV: Battlefield)
The Umbrella Man: After he rewrote her history, Elizabeth Klein referred to him as such given she was not aware of his identity. (AUDIO: UNIT: Dominion)
Professor: This was what Ace constantly called him.
John Doe: The customary name in America for an unidentified human male was applied to the apparently dead Doctor by the staff of Walker General Hospital, and he was given a "John Doe" toe tag before being wheeled into the morgue's freezer, where he subsequently regenerated into his eighth incarnation. (TV: Doctor Who)

Eighth Doctor

Doctor Bowman/James Alistair Bowman: Dr. Grace Holloway came up with this name for the Eighth Doctor whilst introducing him to others. (TV: Doctor Who) The Doctor subsequently used this alias on occasion, filling it out to James Alistair Bowman. (PROSE: Seeing I)
Evergreen Man: The name given to him by the Sidhe. (PROSE: Autumn Mist)
Skipper: The Doctor's companion Samson Griffin always referred to him as such. (AUDIO: Terror Firma)

Ninth Doctor

Mr Spock: Rose Tyler, annoyed with the Ninth Doctor not telling her his name, introduced him to Captain Jack as Spock, after the character of the same name from Star Trek. (TV: The Empty Child)
The Oncoming Storm: The Daleks also referred to the Doctor as the Oncoming Storm in the myths of their homeworld, as noted by his ninth incarnation, indicating that the Daleks feared him. (TV: The Parting of the Ways)

Tenth Doctor

Merlin: The Tenth Doctor would later claim that he was called Merlin by King Arthur. (COMIC: Fugitive)
The Oncoming Storm: Used by Rose when trying to threaten the Clockwork Droids in freeing her and Mickey, only to fail when the Doctor arrived, apparently drunk, as a distraction. (TV: The Girl in the Fireplace)
Spaceman: Donna Noble often called The Doctor by this name and Christina de Souza also referred to the Tenth Doctor by this as well. (TV: The Fires of Pompeii, Planet of the Dead (TV story))
Sweetie, Pretty Boy: Used by River Song the first time he meets her from his point of view. (TV: Silence in the Library / Forest of the Dead)
The Destroyer of Worlds: The Tenth Doctor was called this by Davros whilst destroying the New Dalek Empire; this declaration seemed to truly affect the Doctor as his expression changed drastically after hearing it. (TV: Journey's End)

Eleventh Doctor

The Raggedy Doctor: (also, Raggedy Man) A nickname given to the Eleventh Doctor by Amy Pond. Amy told other people in Leadworth and they referred to him in this way when they met him. (TV: The Eleventh Hour) Amy also called him "Raggedy Man" in The Big Bang , The Girl Who Waited and The Angels Take Manhattan.
Caesar: A Roman Auton, under the influence of River Song's Hallucinogenic lipstick, in 102 A.D., mistook the Doctor for Caesar. (TV: The Pandorica Opens)
Sweetie: Frequently used by River Song as a dual greeting and affectionate nickname.
My Thief, My Beautiful Idiot: Names given to the Doctor by the spirit of his TARDIS during their brief time together when House took over the empty shell. (TV: The Doctor's Wife)
Time Boy: Used by Mels, the second incarnation of River Song, as she anticipated meeting the Doctor while growing up with her parents in Leadworth. (TV: Let's Kill Hitler)
Predator of the Daleks: Whilst not specific to the Eleventh Doctor, it was used as a designation by the Daleks. (TV: Asylum of the Daleks)
Chin-Boy: Oswin Oswald calls the Eleventh Doctor this when encountering him on the Dalek asylum. (TV: Asylum of the Daleks)
Clever Boy: Called this by Oswin's incarnations as well. (TV:Asylum of the Daleks, The Snowmen)
The Mad Monk: Called this by the public in 1207 Cumbria, although it was noted that he was "definitely not a Monk." (TV: The Bells of Saint John)

Behind the scenes

The first edition of the behind-the-scenes book The Making of Doctor Who, published in 1972, stated that the Doctor's name was "δ³Σx²". This has never been confirmed in any Doctor Who narrative, but these letters do appear on the plinth in the Tomb of Rassilon in TV: The Five Doctors. They are also seen on K9's regeneration unit in TV: Regeneration.
During Comic-Con 2012 Steven Moffat, the head writer, has confirmed he knows what The Doctor's real name is, however it is unknown when it will be revealed. Rumours suggest that is what th 50th Anniversary will revolve around.