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The Second Dalek War was a war between the Daleks and humanity. It was one of a series of conflicts which became known as the Dalek Wars.
Origins
In the 26th century, following the human-Draconian War, the Dalek Empire tried to manipulate the rival empires of Earth and Draconia into another war. The Daleks allied themselves with the Master and supported him with Ogrons, using hypnosound technology to trick humans and Draconians alike into thinking the other empire was attacking. They also quietly conquered the planet Spiridon and began experiments to turn their armies invisible; an army of ten thousand Daleks awaited this treatment. However, the Third Doctor exposed their plan, helped General Williams and the Draconian Prince escape from the Master's custody and sent a message to the Time Lords to take him to the Dalek army. With the help of a group of Thals, the Doctor prevented the Daleks from retrieving the army. (TV: Frontier in Space, Planet of the Daleks)
Once the Earth and Draconian Empires learned it was the Daleks disturbing the peace, war was declared on the Dalek Empire.
The War
The Second Dalek War was a vicious conflict that ravaged many worlds and lasted decades. Earth's government enacted emergency powers that allowed it to commandeer personnel, resources and ships from powerful human corporations. (PROSE: Love and War, Return of the Living Dad, Deceit) Earth would give its worst criminals the choice of execution or becoming highly-armed Dalek Killer soldiers. (COMIC: Abslom Daak... Dalek Killer)
There was a generation born into the war unable to imagine anything else. They were called the Dalek Generation. Dalek Bounty Hunters were also hired and rewarded for every Dalek eyestalk they brought back to confirm the kill. (PROSE: Prisoner of the Daleks)
The End of the War
After decades of fighting, the Daleks found they were losing. They tried to use the Arkheon Threshold, a rift in time above a planet they had destroyed decades earlier during the First Dalek Incursion, planning to use the rift to wipe out humanity throughout time so the human race never existed. They used human prisoners to dig through the crust of the planet to reach the Threshold.
When the TARDIS jumped a time track, the Tenth Doctor found himself on the planet Hurala during the war. After capturing a Dalek prisoner, he loosely joined forces with a crew of Dalek Bounty Hunters on-board the Wayfarer, a ship commanded by a Space Major who had deserted, Jon Bowman. About the same time, the people of the planet Auros learned of an approaching Dalek fleet. The population destroyed their planet with Osterhagen technology and fled before the Daleks arrived. However, it was all a trap. The Daleks waited for the refugee fleet to come to them and the Dalek Inquisitor General, Dalek X, ordered the citizens sent to work in the Arkheon mines.
The Wayfarer crew interrogated their Dalek prisoner. The Doctor extracted - he believed - the Daleks' plan to use the Arkheon Threshold to achieve victory. He did not realise the Daleks had already found the Threshold until it was too late. The crew and he were taken prisoner on Arkheon and the Doctor admitted who he was. Dalek X arrived to subject the Doctor to torture and extract Bowman's brain to learn how to bypass Earth's defence systems.
The Doctor explained that the Daleks did not have the technology to use the Threshold but Dalek X thought the Doctor's TARDIS would allow their plan to succeed. The Doctor took Dalek X to Hurala, using the TARDIS as a lure, where Bowman, Koral and he escaped due to Cuttin' Edge attacking a Dalek and being exterminated. The Doctor detonated the abandoned fuelling station on Hurala, destroying all the Daleks as well as Dalek X's flagship, the Exterminator. The loss put a huge dent in the Dalek war machine. Earth pushed back their fleet and the Dalek Empire surrendered shortly after. Dalek X was knocked down a gantry and survived the explosion, though was badly damaged and unable to escape. The Doctor visited him after receiving his transmission, but said nobody else would, the Dalek Fleet was in disarray, and that he had sealed the Threshold. (PROSE: Prisoner of the Daleks)
For the victorious Earth Central forces, the result also led to a major restructuring of humanity's intergalactic government. The corporations, formerly masters of human colonies across explored space, had suffered as a result of the Human-Draconian War, the Dalek Plague and the harsh rule enforced on them by Earth's rulers. Advances in communications technology helped Earth occupy the vacuum left by the corporations' rule, and historians such as Galactic Federation Archivist Ven Kalik agreed the seeds of the later Earth Alliance and Earth Empire were sown in the Second Dalek War. (PROSE: Deceit)