The Second Dalek War was the a war between the Daleks and Humanity. It was part 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 think the other empire was attacking. They also quietly conquered the planet Spiridon and began experiments to turn their armies invisible; an army of 12,000 Daleks awaited this treatment. However, the Third Doctor exposed their plan, helping General Williams and the Draconian Prince escape from the Master's custody, and he sent a message to the Time Lords to take him to the Dalek army. With them help of a group of Thals, the Doctor was able to prevent the Daleks from retrieving the army. (DW: Frontier in Space, Planet of the Daleks)
Once the Earth and Draconian Empires learned it was in fact 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. (NA: Love and War, Return of the Living Dad, Deceit) The situation was grim enough that Earth would give its worst criminals the choice of execution or becoming highly-armed Dalek Killer soldiers. (DWM: Abslom Daak... Dalek Killer)
There was a generation born into the war that did not know what it was like not to live in the time of the conflict. They were referred to as the Dalek Generation. Dalek Bounty Hunters were also hired and rewarded them for ever Dalek eyestalk they brought back to confirm the kill. (NSA: Prisoner of the Daleks)
The end of the War
After decades of fighting, the Daleks surpringly found they were losing. To ensure a victory, the Daleks attempted to utilise the Arkheon Threshold, a rift in time above a planet they had destroyed decades earlier during the First Dalek Incursion. They planned to use the rift to wipe out Humanity throughout time so that the human race never existed. They used human prisoners to mine through the crust of the planet to reach the Treshold.
When the TARDIS jumped a time track, the Tenth Doctor found himself on the planet Hurala, back in the time of the war. After capturing a Dalek prisoner, he loosely joined forces with a crew of Dalek Bounty Hunters on-board a ship called the Wayfarer led by a deserter Space Major, Jon Bowman. Round about the same time as the Doctor's arrival, the people of the planet Auros learned of an approaching Dalek fleet. The population destroyed their planet using Osterhargen 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 citizents to be sent to work in the Arkheon mines.
The Wayfarer crew interrogated their Dalek prisoner about the Daleks' plan, and the Doctor was able to extract - he believed - the Daleks' plan to use the Arkheon Threshold to achieve their victory. He did not realise that the Daleks had already found the Treshold until it was too late. He and the crew were taken prisoner. Dalek X arrived to subject the Doctor to torture and they planned to extract Bowman's brain to learn how to bypass Earth's defence systems.
Finally, the Doctor explained that the Daleks did not have sufficient technology to use the Treshold properly, but Dalek X thought the Doctor's TARDIS would be what they needed for their plan to succeed. The Doctor took Dalek X to Hurala, using the TARDIS as a lure, where he, Bowman and Koral escaped. The Doctor was able to detonate the disused fuelling station on Hurala, destroying all the Daleks as well as Dalek X's flagship, the Exterminator and all it's provisions. The loss of such a powerful Dalek vessel put a huge dent in the Dalek war machine. Earth was able to push their fleet right back and the Dalek Empire surrendered shortly after. (NSA: Prisoner of the Daleks)