Doctor Who and the Invasion from Space was a forty-six-page novella published in 1966 in the same format as the Doctor Who annual releases. It stands as the first officially published original (i.e. non-TV-based) long-form text story to feature the Doctor. It proved to be an anomaly of Doctor Who prose fiction. No other original fiction books would be published until 1980, when the children's The Adventures of K9 short story series debuted. After that, only the novels Harry Sullivan's War and Turlough and the Earthlink Dilemma followed in the 1980s. It was not until 1991's launch of the Virgin New Adventures line that the Doctor himself returned to original fiction published as a standalone novel.
The Doctor is joined at the beginning of the story by the Mortimer family, who are fleeing the Great Fire of London.
They then land on a spaceship driven by a super-computer and carrying survivors from Andromeda who are planning an invasion of the galaxy.
The TARDIS is being buffeted by a space storm: to add to the Doctor's annoyance, he is accompanied by Helen and George Mortimer and their children, Ida and Alan. The TARDIS had previously materialised in a pig sty during the Great Fire of London on 2 September 1666: the Doctor reluctantly rescued George, a swineherd, and his family from the flames, and now they are convinced he is a warlock, possibly come to conduct them to hell.
When the storm has passed, the TARDIS has materialised on a planetoid that should be too small to retain its breathable atmosphere: the Great Spiral Nebula of Andromeda, the galaxy called M.31 on Earth, fills much of the sky. The travellers are welcomed by blond humanoids (George mistakes them for angels) who call themselves Aalas, and invite them to meet the One.
The party descends into the ground: the Doctor realises that the planetoid is a vast space vessel. Nearer the planetoid's centre, where gravity is lighter, they are taken to a room with a glass-like panel, behind which the One hails them as Men of the Milky Way. The One explains that it was made by the Men of Andromeda, extinct for millions of years, and that, to the Doctor's incredulity, it now rules the galaxy. The Doctor's attempt to look behind the panel is painfully rebuffed, and the party is led away to a beautifully prepared meal.
The Aalas explain that all the food has been been synthesised, as they sustain themselves by electricity and radiation: the Doctor realises they are androids. They explain that the One is the entire vessel: it made them and they believe it to be omnipotent. At the One's command, they carry the protesting Doctor back to the screen room, where the One has succeeded in opening and examining the TARDIS. It has identified it as a space-time vessel, but notes that it is inert without a missing component, which the Doctor proudly informs it is himself: his "spirit and nature are built into it". The One agrees and instructs him to demonstrate its operation. On the Doctor's refusal, it begins to gibber and malfunction. Recovering quickly, it apologises, explaining that the Doctor's disobedience is the first it has experienced in a billion years. The One tells him that that it is leading a migration from Andromeda to the Milky Way, which will take another three hundred million years to arrive. The TARDIS technology would enable the journey to be made instantaneously. To obtain the Doctor's cooperation, it offers access to its Diagrams of power, which map the entire Milky Way throughout its lifespan.
The Doctor deliberately reiterates his defiance and, taking advantage of the One's subsequent breakdown, which also incapacitates the Aalas, he runs into the TARDIS and dematerialises, leaving the Mortimers to their fate. The TARDIS takes him to many of the million worlds of the One's armada, dizzying him with the variety of the Andromedan life flourishing on them, and eventually returns him to the One's audience room. Defeated, the Doctor supposes that the One has retrieved him, but the One, amused, says that the power that brought him back will be its main ally in securing the Doctor's compliance. It explains that the Andromeda galaxy is approaching a region of space inimical to life, necessitating the migration. On arrival, the species of the Milky Way will be exterminated, to make room for the Andromedans. Accepting that the technology of the TARDIS cannot be used or duplicated, the One instead resolves to keep the Doctor's brain alive for the duration of the voyage for its knowledge and insight. It also expresses pleasure at the behaviour of the primitive Mortimers, and the Doctor realises that the force that drew him back was his subconscious loyalty to them as fellow living beings. When the Mortimers are brought back to the TARDIS, he prepares, without much hope, to attempt another escape, but Ida, enraged that there is no more jelly to eat, throws her bowl at the One's screen in a tantrum, breaking it and damaging the circuitry behind it.
The One, psychologically unable to cope with physical violence against itself, goes into a terminal breakdown, shutting down the Aalas. The Doctor attempts to take the Diagrams of power, but they dissolve into light at his touch. The Andromedan armada is left to drift, unnavigated, through space. Reflecting that the One only fought to protect its own, as it had been programmed, the Doctor leaves in the TARDIS with the Mortimers.
"What's a galaxy?" asks Ida. "That's the prettiest word I ever heard." "Do you know," replies the Doctor, "one of these days I'm going to have a look for myself."
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- The Doctor has "very seldom...been able to predict where or when his Tardis would materialise." It is implied that the TARDIS responds to the Doctor's subconscious desires.
- The Doctor is referred to as Dr Who throughout. It is implied that he comes from Earth.
- The One, who learns more about the TARDIS than the Doctor knows to begin with, agrees that it will not operate without him, confirming the Doctor's claim in TV: Pyramids of Mars that its controls are isomorphic.
- Later in his personal timeline, the Doctor would return to the Great Fire of London on two occasions. During the latter visit, in his fifth incarnation, he would learn that the fire started when a Terileptil weapon overloaded in a bakery on Pudding Lane and that he himself played a major role in these events. (TV: The Visitation) Ironically, the Fourth Doctor arriving shortly before his future self's departure, was wrongly accused of starting the fire only hours later. It is possible that, for a brief period after the First Doctor's arrival in 1666, that there were three separate incarnations of the Doctor co-existing in the same timeframe and in close promixity to one another. (TV: Pyramids of Mars, PROSE: The Republican's Story) His involvement in the fire remained a source of embarrassment for the Doctor in his sixth incarnation. (AUDIO: Point of Entry, The Marian Conspiracy, Doctor Who and the Pirates)
- The renegade Time Lady Iris Wildthyme would later claim to have been present for the Great Fire. (AUDIO: Excelis Dawns)