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
At one point, 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
 * Find some intrinsic flaw or weakness to exploit in the Daleks

Several events that 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. (BBCR: The Dalek Conquests)

The Daleks eventually learned of what the Time Lords tried to do, 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 that these were merely 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 first Dalek attack on Gallifrey, known as the Etra Prime Incident, began an escalation of hostilities. (BFA: The Apocalypse Element) Lady President Romana made diplomatic overtures. (NA: Lungbarrow) She initiated a Dalek-Time Lord peace treaty under the Act of Master Restitution. (DWAN: 2006 Doctor Who Annual)

The Daleks launched over a thousand ships into the Time Vortex, These forces were stopped by the Eighth Doctor, who left them trapped in the vortex. (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. Over a million Battle TARDISes were used by the Time Lords. (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 of legends that it was the Doctor who led the Time Lords into battle. (DW: The Sontaran Stratagem)

During the very 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 managed to time shift back into the war and extract Davros from the time-locked event, at the cost of his sanity, transporting him into the post-war universe. (DW: The Stolen Earth, Journey's End)

During the course of the war, the entire chain of Hotel Historia was destroyed (DWM: Hotel Historia) and the Nestene Consciousness's protein planets were destroyed (DW: Rose), including Polymos TDL: The Dust of Ages) Kolox was destroyed at some point, leaving behind the Kolox Nebula. (DWA: The Skrawn Inheritance) Another of the known 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 also resurrected the Master, believing him to be 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) At a later point in the war, Rassilon was President and lead 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 0.5 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, a plan in which the Time Lords would ascend to become creatures of pure consciousness, but in so doing would destroy all of creation. 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 described the war in its final days as "hell." (DW: The End of Time)

Conclusion
In the final days of the War, the Eighth Doctor attempted 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 escape 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 that 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 device 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 that the universe convulsed as many planets, systems and galaxies were consumed. (IDW: Agent Provocateur)

When the Doctor used the Moment the war became 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, was somehow able to do so, albeit at the cost of his sanity. (DW: The Stolen Earth) The Time Lord High Council attempted to escape the Time Lock by implanting a signal in the head 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, but were defeated by the Tenth Doctor and the Master, who aided the Doctor when he realised how much he had been manipulated. (DW: The End of Time)

According to the Tenth Doctor, the time-lock prevented him from going back and saving his people. (DW: The Fires of Pompeii). This may have been an excuse; while he has hinted that the idea occurred to him (DW: Father's Day), he also said that the Time War changed his people beyond recognition and that 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 the time-aware "higher" ones. The Time Lords were thought of as myths by the higher species, like the Forest of Cheem. (DW: The End of the World, The Stolen Earth)


 * The Nestene Consciousness justified its 2005 invasion of Earth by the loss of its protein planets. (DW: Rose)
 * The Gelth lost their physical bodies because of the war, reduced to gaseous forms. (DW: The Unquiet Dead)
 * The Eternals apparently fled this reality in despair, never to be seen again and the Greater Animus died in the conflict. (DWAN: 2006 Doctor Who Annual)
 * 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 since 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 itself more vulnerable to change. The Ninth and Tenth Doctor 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's life 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 stated 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 Doctor's survival may have entailed a regeneration from the Eighth Doctor into the Ninth Doctor.


 * 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, and it is known 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 lone Dalek survived and crashed on Ascension Island on Earth in 1962, In 2012, it self-destructed when it regenerated its injuries by absorbing Rose Tyler's DNA, causing it to mutate 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 Cult of Skaro and the Daleks imprisoned within 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 located by a band of impure Daleks that 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)
 * Three groups of Time War era Daleks arrived on Earth in different points in its history, wreaking havoc, although it is unknown if they actually were survivors.
 * An army of Daleks were weakened and fell through time to 70 million years before the 21st century and were destroyed by dinosaurs. (DWBIT: #51)
 * 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. (DWBIT: #11) They may possibly be the same group as a group of Daleks which massacred the Pirate fleet of Captain Jack Lawrence in late September 1697. (DWBIT: #19)
 * A group of Daleks appeared in the 22nd century and stole a Krikoosh cage to turn all humans into living ghosts so they would be unable to fight back against the Daleks. The Daleks attempted 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)

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 during 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 often referred to as "the Last Great Time War."