In one palimpsest reality which the personal timelines of the Doctor and the Dalek race passed through following the Last Great Time War, (PROSE: The Time Traveller's Almanac) the Ninth Doctor and his companion Rose Tyler encountered what the former believed to be the last surviving Dalek in existence in captivity in Henry van Statten's vault in 2012, (TV: Dalek) in what became known as the Van Statten Incident. (PROSE: Dalek Combat Training Manual) Named "the Metaltron" by van Statten, this Dalek was unfamiliar to its human captors. (TV: Dalek)
History
Nature
In the overarching span of overtime, there existed a history of history's writing, rewriting, and overwriting. (PROSE: The Gallifrey Chronicles) Savar discovered the true nature of the Prime history as existing atop infinite overwritten palimpsest universes. As time was rewritten, new histories emerged which replaced the old ones and consigned them to the margins of existence. As a whole, this meant that the Doctor's universe was "riddled with paradox and contradiction likes weevils in a biscuit." (PROSE: The Infinity Doctors)
Professor Arthur Candy believed that the Doctor, being a Complex Space-Time Event, warped reality around him without even needing to make explicit alterations via time travel. As such, "like all [CSTEs], he [could] not easily be studied because his very presence alters the way you think". (PROSE: Continuity Errors)
A day to come
During the era of the Last Great Time War, the reality of what the Time Lords dubbed the Van Statten Incident among other events from the post-Time War universe was observed by them as an extrapolation of the possible future from the Matrix. (PROSE: Dalek Combat Training Manual)
The Metaltron
At the time of the incident, the Doctor believed that both the Time Lords bar himself and the Daleks had been wiped out at the end of the Time War, to the point that he initially took the sight of the lone Dalek on Earth in 2012 to be "impossible". This lone Dalek survivor, who was skeptical as to the Doctor's account of the war's end, searched for traces of its kind by scanning Earth's internet, satellites and radio telescopes, only to find "nothing". (TV: Dalek)
In the aftermath of the incident, the BBC Radio documentary The Dalek Conquests covered notable confrontations between the Doctor and the Daleks. The narrator of the documentary was aware that, following their encounter with the Metaltron, the Doctor and Rose discovered that the Dalek Emperor had also survived the Time War as he launched a new invasion of Earth in the year 200,100 only for him and his Dalek Fleet to be wiped out by Rose as the Bad Wolf. This event was placed by The Dalek Conquests as the end of known Dalek history, however, the narrator did ponder openly as to whether a species with access to time travel could ever truly go extinct. (AUDIO: The Dalek Conquests, TV: The Parting of the Ways)
Fate
In his next incarnation, the Doctor was in Torchwood London in 2007 when the Cult of Skaro emerged from the Sphere within the Void and precipitated the Battle of Canary Wharf (TV: Army of Ghosts/Doomsday) before going back in time and influencing the construction of the Empire State Building for their own ends, (TV: Daleks in Manhattan/Evolution of the Daleks) also being indirectly responsible for the Earth being transported to the Medusa Cascade. (TV: The Stolen Earth/Journey's End) In the earlier "Metaltron" reality, however, the personal timelines of both the Doctor and the Daleks' had not progressed to the point where those events occurred. This meant that, at the time of the Van Statten Incident, the Cult of Skaro was still inside their Sphere within the Void. (PROSE: The Time Traveller's Almanac) Indeed, the Doctor himself was aware that the Sphere was designed to exist outside time and space. (TV: Doomsday)
The Eleventh Doctor also became aware that the memory of the Dalek invasion of Earth within the Medusa Cascade had been lost to the cracks in time (TV: Victory of the Daleks, Flesh and Stone) caused by the Total Collapse Event Incident. Though the Doctor initiated Big Bang Two to "reboot" the universe after it had been all but destroyed by the total event collapse, (TV: The Big Bang) the Time Lords observed that Big Bang Two itself caused subtle changes in the timeline of the planet Earth such that humanity at large would remain unfamiliar with the Daleks as evidenced during the Security Drone Incident of 2021. (PROSE: Dalek Combat Training Manual, TV: Revolution of the Daleks)
Behind the scenes
At this point in their timelines, the Doctor and this Dalek seemed to be the only survivors of the Last Great Time War - the last of their races. The Cult of Skaro were still inside their sphere in the Void and had yet to emerge in the Torchwood Institute and precipitate the Battle of Canary Wharf in 2007. The Empire State Building had been constructed without their interference, and the Earth had never been transported across the universe to the Medusa Cascade. Like Henry van Statten, most of the human race had no idea what a Dalek was. With the death of the last Dalek, the Doctor was the unwilling victor of the Time War. Or so he thought...