Last Great Time War

The Time War — or, as the Tenth Doctor specified to Martha Jones in New New York, the Last Great Time War — was the war between mighty races, including the Time Lords and the Daleks "for the sake of all creation". It resulted in the destruction of Gallifrey, leaving only two Time Lords and a small number of Daleks as survivors.

Origins
The Time Lords predicted that in one possible timeline, the Daleks would "destroy all other life forms and make themselves the dominant creature in the universe." The Time Lord Ferain sent the Fourth Doctor on a mission to Skaro during the Thousand Year War with certain objectives: The Doctor believed he might have set back the history of the Daleks for a thousand years. (DW: Genesis of the Daleks)
 * If possible, to avert the creation of the Daleks
 * Otherwise to alter their development and make them less aggressive
 * To find some intrinsic flaw or weakness to exploit in the Daleks

Several key events occurred even before the Fourth Doctor's interference. These, including the Daleks' achievement of time travel with the TARDIS-esque Dalek time machine (DW: The Chase) and the Time Lords helping the Third Doctor navigate his TARDIS to Spiridon, (DW: Planet of the Daleks) were early shots fired in the Time War. (AG: The Dalek Conquests)

The Daleks learned of the Time Lords' efforts and planned to use duplicates of the Fifth Doctor and his companions to assassinate the High Council of the Time Lords. These duplicates were killed when the station they were on was destroyed. (DW: Resurrection of the Daleks) One of the Dalek Puppet Emperors declared hostilities, although the Daleks claimed these were in retaliation for the Time Lords sending the Fourth Doctor back in time to prevent their creation.

Later, the Seventh Doctor used the Hand of Omega to apparently destroy the Dalek homeworld of Skaro. (DW: Remembrance of the Daleks)

The Daleks launched over a thousand ships into the Time Vortex, These forces were stopped by the Eighth Doctor, who left them trapped there. (BFA: The Time of the Daleks) The Daleks later made a deal with the Time Lords that allowed the Dalek fleet to leave the Time Vortex. (BFA: Neverland)

The conflict
The main force was made of a fleet of Dalek Flying Saucers which had a total of ten million. The Time Lords used over a million Battle TARDISes. (NSA: Peacemaker)

The Eighth Doctor joined the Time Lords in the fight against the Daleks after witnessing the death of a child at the hands of a Dalek. (ST: Museum Peace) The Sontarans told legends of the Doctor leading Time Lords into battle. (DW: The Sontaran Stratagem)

In the first year Davros was killed at the Gates of Elysium when his command ship flew into the jaws of the Nightmare Child. The Doctor tried to save him, but failed. Eventually, Caan, the last survivor of the Cult Of Skaro time shifted back into the war and saved Davros from the time-locked event at the cost of his own sanity, bringing him into the post-war universe. (DW: The Stolen Earth, Journey's End)

During the war, the entire chain of Hotel Historia was destroyed, (DWM: Hotel Historia) Polymos was destroyed, (TDL: The Dust of Ages) and Kolox was destroyed, leaving behind the Kolox Nebula. (DWA: The Skrawn Inheritance) Another of the battlefields was Arcadia, where the Doctor fought. (DW: Doomsday) At the heart of the war, millions died every second. (DW: The End of Time)

The Time Lords resurrected the Master, believing him an excellent soldier. The Master was at the Cruciform, but when the Dalek Emperor took control of it, he ran in fear. (DW: The Sound of Drums) Later in the war, Rassilon was President and led the battle to save Gallifrey. (DW: The End of Time)

Toward the end of the war the Daleks sent a capsule to Earth in the year 70 to spread the Dalek Factor amongst humans. The capsule's engine exploded and the Dalek was killed soon after impact. It released only a small amount of the Dalek Factor, leading to only one in five hundred million humans having it. (QR: I am a Dalek)

By the end of the war, President Rassilon was so desperate he proposed the Ultimate Sanction. The Time Lords would become creatures of pure consciousness and all of creation would be destroyed. Other horrors and terrors seen in the final days of the war (including the Daleks) were the Deathsmiths of Goth, the Skaro Degradations, the Horde of Travesties, the Could've Been King and his Army of Meanwhiles and Neverweres and the Nightmare Child. The Tenth Doctor called the war in its final days "hell." (DW: The End of Time)

Conclusion
In the final days of the War, the Eighth Doctor tried to regain the Great Key, which had been stolen by unknown forces. After being imprisoned for a month, with the help of Chantir he overpowered the guards and escaped with the key. With the key, he believed that the De-mat Gun could be replicated and the Medusa Cascade closed. The Doctor planned to modify the gun so instead of it removing an individual from time and space, it would remove millions. (IDW: The Forgotten) This modified De-Mat Gun became the Moment, the weapon that would destroy Gallifrey. (DW: The End of Time, IDW: Don't Step on the Grass) The Doctor destroyed Gallifrey because Lord President Rassilon planned to destroy time so the Time Lords could become non-corporeal beings, existing without time. (DW: The End of Time) With the exception of a very few survivors, the Time Lords and the Daleks disappeared from time and space. (DW: Dalek, The Parting of the Ways, Army of Ghosts/Doomsday)

Gallifrey was destroyed in a silent flash as bright as a sun. Its annihilation was so profound it stretched deep into the past and far into the future. (NSA: The Eyeless) The Cruciform fell when Gallifrey was destroyed. (IDW: The Forgotten) The blast was so powerful the universe convulsed as planets, systems and galaxies were obliterated. (IDW: Agent Provocateur)

When the Doctor used the Moment, the war was time-locked, (IDW: Don't Step on the Grass) making it (in theory, or at least according to the Tenth Doctor) impossible to revisit the events; Dalek Caan, however, somehow entered, albeit at the cost of his sanity. (DW: The Stolen Earth) The Time Lord High Council tried to escape the Time Lock by implanting a signal in the mind of the Master when he was a boy and sending a White Point Diamond to late 2009 Earth. On the last day of the war, five Time Lords including Rassilon and the Woman escaped to Earth in 2009. They were defeated by the Tenth Doctor and the Master, who saved the Doctor when he realised how he had been manipulated. (DW: The End of Time)

According to the Tenth Doctor, the time-lock prevented him going back and saving his people. (DW: The Fires of Pompeii). This may have been an excuse; while he hinted that the idea occurred to him, (DW: Father's Day) he also said that the Time War changed his people beyond recognition and he felt forced to stop them after learning about Rassilon's Ultimate Sanction. (DW: The End of Time)

Aftermath
The war was mostly invisible to "lower species", but devastating to time-aware "higher" ones. The Time Lords were thought of as myths by higher species like the Forest of Cheem. (DW: The End of the World, The Stolen Earth)


 * The Gelth lost their physical bodies because of the war. They were reduced to gaseous forms. (DW: The Unquiet Dead)
 * Though the Sontarans were aware of the war, they weren't allowed to take part (DW: The Sontaran Stratagem), as opposed to the Graxnix who were one of the lowest races to take part. (DWM: Hotel Historia)
 * It is possible that Eve's species was wiped out in the Last Great Time War; she mentioned two races (possibly the Time Lords and the Daleks) and her planet being "Exterminated", which is what Daleks would say, because her people were time-sensitive. (SJA: The Mad Woman in the Attic)

The destruction of the Time Lords created a vacuum that may have left history more vulnerable to change. The Ninth and Tenth Doctors explained to Rose Tyler and Donna Noble that time was in flux and history could change instantly -- a big change from the way it had been. (DW: The Unquiet Dead, The Fires of Pompeii)

The most dramatic demonstration of this was when Rose created a temporal paradox by crossing her own time stream to save her father just before his death in a traffic accident. This summoned the Reapers, who descended to sterilise the "wound" in time by devouring everything in sight. The Ninth Doctor said that if the Time Lords had been still around, they could have held back the Reapers and prevented or repaired the paradox. (DW: Father's Day)

As well, the Tenth Doctor noted that when the Time Lords were around, travel between Parallel worlds was less difficult. With their demise, the paths between worlds were closed. (DW: Rise of the Cybermen)

Gallifrey inhabitants

 * The Doctor; he stated in his ninth body that if any other Time Lords lived, he would have sensed their presence. (DW: Dalek)
 * The Master also survived, having used a Chameleon Arch to become the human Professor Yana to escape the war. His use of the arch prevented the Doctor from sensing his existence. (DW: Utopia)
 * Whilst not a Time Lord, Leela was a resident of the Capitol on Gallifrey. She survived for at least a short time after the destruction of Gallifrey. (CC: The Catalyst)
 * K9 Mark I survived the destruction of Gallifrey before travelling through time to the year 2050 and "regenerating." (K9TV: Regeneration)

Daleks

 * A single Dalek survived and crashed on Ascension Island on Earth in 1962. In 2012, it self-destructed when it healed its injuries by absorbing Rose Tyler's DNA, mutating into something impure. (DW: Dalek)
 * The Dalek Emperor also survived. He had fallen through time to approximately the 2,000th century and set about re-building an army from the DNA of humans. He was destroyed by Rose Tyler with the power of the time-vortex. (DW: The Parting of the Ways)
 * The Daleks sent a time capsule to 70 AD Earth in order to spread the Dalek Factor amongst the humans. The Tenth Doctor and Rose killed the Dalek. (QR: I am a Dalek)
 * The Cult of Skaro and the Daleks imprisoned in the Genesis Ark escaped the attentions of the Bad Wolf, having left the universe for the Void before the end of the war. The imprisoned Daleks were sucked back into the Void, but the Cult escaped into 1930 Manhattan, where most of them died. Dalek Caan survived this encounter but was presumably killed when the Crucible was destroyed by the Meta-Crisis Tenth Doctor. (DW: Doomsday, Evolution of the Daleks, Journey's End)
 * A Dalek Progenitor device survived the war and was found by a band of impure Daleks which had survived a battle with the Tenth Doctor. With the Eleventh Doctor's "testimony" that the impure Daleks were, in fact, real Daleks, the Progenitor created the New Dalek Paradigm. (DW: Victory of the Daleks)
 * A group of Daleks that appeared to be Time War era appeared in the 22nd century and stole a Krikoosh cage to turn all humans into living ghosts so they would be unable to fight the Daleks. The Daleks tried to signal all remaining Daleks in the universe. They were defeated by the Tenth Doctor with the help of the Krikoosh. (DWBIT: The Living Ghosts, Extermination of the Daleks)
 * Several Daleks who had survived several pre-Time War encounters with the Doctor, such as on Kembel, Aridius and Vulcan resided in the Dalek Asylum. (DW: Asylum of the Daleks)

Others

 * Though Davros was believed by the Doctor to have been killed in the war (consumed by the Nightmare Child), Dalek Caan temporal shifted into the war and rescued him. He presumably died when the Crucible was destroyed. (DW: The Stolen Earth, Journey's End)
 * The Advocate escaped the Time War when Davros was rescued by Dalek Caan. (IDW: Fugitive, Don't Step on the Grass)
 * Eve was sent to Earth as a child to survive extermination in the Time War. Her species was time-sensitive, a threat and was exterminated, presumably by the Daleks. It is not known if she had to break through the time-lock, if the Daleks broke through it to kill her species or if they were killed before the war was time locked. (SJA: The Mad Woman in the Attic)
 * The Gelth survived but lost their bodies. (DW: The Unquiet Dead)

Behind the scenes

 * A 2005 faux-documentary produced by BBC Radio, The Dalek Conquests, attempts to put the Time War into context with the Doctor's recurring conflicts with the Daleks over the years.
 * A long-running story arc featured in the BBC Eighth Doctor Adventures book series concurrent with the return of Doctor Who to television in 2005 featured another Time War, the Second War in Heaven between the Time Lords and the Enemy. Russell T Davies, the producer of the revived TV series, has, however, been on record as stating that the Second War in Heaven is a different conflict, which is one reason why the war referenced on TV is called "the Last Great Time War."

Doctor Who: Battles in Time
Non-narrative material in Doctor Who: Battles in Time magazine revealed further survivors of the Time War.


 * According to DWBIT 51, an army of Daleks were weakened and fell through time to 70 million years before the 21st century and were destroyed by dinosaurs.
 * According to DWBIT 11, a Dalek ship crashed in an island in the western part of the North Atlantic Ocean, causing a disturbances in human vehicles and the mysterious disappearances of aircraft and surface vessels. Their ultimate fate is unknown.

Also, DWBIT 19 stated a group of Daleks massacred the pirate fleet of Captain Jack Lawrence in late September 1697.