Dalek invasion of the galaxy

Human historians, who wrote in the post-Time War universe after the Siege of Trenzalore, understood that a full-scale Dalek invasion of the galaxy of Mutter's Spiral. According to those humans, this invasion was launched after the failure of the Exxilon initiative, but the Time Lords stated this invasion was launched by the post-Time War Dalek Empire after the Siege of Trenzalore.

Background


The Exxilon Gambit was the final action of the Third Dalek War, (PROSE: The Secret Lives of Monsters) which followed the 26th century Second Dalek War. (COMIC: Pureblood) The Time Lords identified the Exxilon Incident as taking place in the late 27th century. (PROSE: Dalek Combat Training Manual) However, human historians postdating the Siege of Trenzalore indicated that the Daleks' germ warfare campaign which culminated with the Exxilon Gambit came multiple centuries following the 26th century Dalek War. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) Similarly another book about universal history seemed to attribute the plague and the Exxilon expedition as stemming from to the Dalek conflict that was sparked in the year 4000 by the attempt to develop the Time Destructor. (PROSE: The Whoniverse)

The Daleks resorted to biological warfare, (PROSE: The Secret Lives of Monsters) which they had previously experimented with during the Spiridon campaign at the start of the last Dalek war. (TV: Planet of the Daleks, PROSE: Remembrance of the Daleks) Utilising plague missiles, the Daleks infected the Earth's Outer World colonies with a deadly outbreak of space plague, (PROSE: The Secret Lives of Monsters) threatening millions of lives, although the Earth forces seemed unaware the Daleks were responsible for the plague. (TV: Death to the Daleks) Indeed, the wider Earth Empire was unaware of any active fighting against the Daleks, with some citizens even coming to believe the exterminators did not really exist and were simply propaganda used to scare citizens into obeying their governments. The outbreak of the plague only exacerbated that skepticism. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)

The Exxilon Gambit took the form of numerous expeditions by opposing parties to the planet Exxilon to acquire the rare mineral of parrinium. Ultimately, the parrinium was claimed by an Earth expedition with the assistance of the Third Doctor, whilst the opposing Dalek expedition was destroyed. (TV: Death to the Daleks) According to human historians, after the events on Exxilon, the Dalek Supreme Council decided that the time for discretion had ended. The galaxy was still reeling from the Daleks' space plague and any further delay would give them time to recover. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)

However, the Time Lords of the Last Great Time War, looking into projections of the Doctor's relative future, dated this Dalek invasion to be in the post-Time War universe. Specifically, the Time Lords said these events occurred after the Siege of Trenzalore. (PROSE: Dalek Combat Training Manual) The siege had been a massive Dalek defeat that ensured the Time Lords could one day return to the universe (TV: The Time of the Doctor) and saw the destruction of the Parliament of the Daleks. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)

The invasion begins
No matter if it was launched in the days before or after the Time War, (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe, Dalek Combat Training Manual) the Dalek invasion was launched and only the continued preparedness of the Combined Galactic Resistance kept them from overrunning the whole of inhabited space in the first assault. The Daleks scoured the life from whole planets. Hospital ships treating plague victims were converted into troop carriers. Conscription was introduced on a thousand worlds. Bitter enemies buried ancient rivalries to unite against the Daleks. The once great empire of Draconia splintered and fell before the Dalek onslaught. Humanity endured, but every day more ground was given and more worlds fell to the Daleks. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)

A Good Dalek
Rusty was a standard Dalek drone until one battle left him drifting alone in the depths of space; unknown to him, his power source had cracked and was leaking radiation that disrupted his shell's programming to keep him from feeling anything but xenophobic hatred towards non-Daleks. Seeing the birth of a star triggered a realisation in Rusty of the inevitability of life returning despite the efforts of the Daleks. From this, Rusty saw Daleks were evil and needed to be wiped from existence. Eventually, he was found by the Combined Galactic Resistance, and brought aboard their ship the Aristotle (TV: Into the Dalek) in the Ryzak solar system. (PROSE: The Secret Lives of Monsters) They attempted to open the shell, hurting Rusty. Badly hurt already, Rusty asked for help in recovering so he could exterminate his own race. Interested in the idea of a moral Dalek, the crew promised him medical attention.

The Doctor, Clara Oswald, Journey Blue, Ross and Gretchen Carlisle were shrunk and ventured into Rusty to try to fix the damage that was killing him. Using his sonic screwdriver, the Doctor repaired a crack in Rusty's power source that was leaking radiation and killing him. However, without the radiation affecting him, Rusty reverted to his original Dalek programming, restored to full power and went on a rampage, killing several soldiers and sending a distress call that attracted a nearby Dalek flying saucer. Upon urging from Clara, the Doctor decided to attempt to restore the changes once more. He had Clara reactivate the Dalek's suppressed memories so he could see the birth of the star again and be reminded of the universe's beauty.

Clara succeeded and the Doctor telepathically linked with Rusty to show him more from inside his own mind. At first it seemed the Doctor had succeeded, as Rusty again saw beauty and divinity. However, Rusty also saw the Doctor's hatred of the Daleks, which resonated even more strongly with him. Rusty saw the Daleks as an evil which must be, in true Dalek fashion, exterminated. Rusty then went on a rampage against his own kind, slaughtering the Daleks attacking the Aristotle and fooling the saucer into retreating by falsely telling the other Daleks that the Aristotle's self-destruct had been activated. Rusty left with the Daleks to continue his efforts against them, telling the Doctor that although Rusty himself was not a "good Dalek", the Doctor was a good Dalek. (TV: Into the Dalek)

Aftermath
According to human historians, Rusty's betrayal sent the Supreme Council in a world of worry, but their experiments proved that his freak turn of heart could not be mass-replicated. Relieved, and unwilling to snuff out such beautiful hatred as Rusty's, they consigned him to the Dalek Asylum, home to Daleks whose hatred was so powerful it threatened their own kind in one way or another. The Daleks began preparations to resume their war against humanity when their time travel experiments resulted in the successful development of a time machine which was used to pursue the Doctor's first incarnation through time which led them to conflict with the Mechanoids on Mechanus, beginning a war which last for centuries before the Daleks prevailed, their advances turning away from Mutter's Spiral and towards the Outer Galaxies, (PROSE:  The Astounding Untold History of the Greatest Enemies of the Universe) where they made a number of gains in the half a millennium leading up to the year 4000, when they launched a new, ill-fated invasion of Earth's galaxy. (TV: Mission to the Unknown, The Daleks' Master Plan)

However, by the Time Lords' understanding, these events had long since happened by the time of Rusty and this invasion. According to them, the Asylum Incident, (PROSE: Dalek Combat Training Manual) which saw the Asylum was destroyed by the Parliament of the Daleks, (TV: Asylum of the Daleks) had already happened as well. (PROSE: Dalek Combat Training Manual)

No matter the case, Rusty survived and continued to fight the Daleks for billions of years. In time, he grew to be, as the Twelfth Doctor put it, "a bit of a legend", entirely because he was a Dalek who had turned on his own kind. As his casing grew ancient and, much like his nickname implied it should be, rusty, (PROSE: Twice Upon a Time) he isolated himself at the centre of the universe on Villengard, combating numerous Daleks that came to kill him. Rusty fended them off, positioning himself in a tower overlooking the battered city, (TV: Twice Upon a Time) specifically remaining in what may have once been a throne room. Hooked up to machines to appeared to be keeping the Dalek alive, Rusty would fire out the windows at the many Daleks who came to destroy him, destroying their casings and filling the ruins with a mess of broken travel machines. (PROSE: Twice Upon a Time) The Twelfth Doctor, nearing his regeneration, came to the lone Dalek with his original incarnation to gain information on the Testimony, taking his leave after the information was received. (TV: Twice Upon a Time)

Behind the scenes

 * According to Lance Parkin's Whoniverse: An Unofficial Planet-By-Planet Guide to the Universe of the Doctor, from Gallifrey to Skaro, the script for Into the Dalek specifies that the story takes place in the 31st century.