The Time War was fought between the Time Lords and the Daleks, resulting in their near-complete destruction, which the series suggests was caused by the Doctor himself. The Doctor also referred to this conflict as "the last great Time War," implying that there had been others.
 The Last Great Time War
The Last Great Time War is first mentioned in the first episode of the 2005 series. There, the Ninth Doctor explains to his companion, Rose Tyler, that the reason behind the invasion of Earth was because its food planets were destroyed. Later in the episode, the Doctor states that he fought in the war, but he was unable to save the Nestenes' planet.
In the following episode, "The End of the World" set five billion years in the future, Jabe expresses amazement that the Doctor, a Time Lord, still exists, signifying that the war had consequences all across time. At the end of that episode, the Doctor confesses to Rose that the War had destroyed his home planet, leaving him the only surviving Time Lord.
In the episode "Dalek", it is revealed that the Time Lords' adversaries in the war were the Daleks. The Doctor claims responsibility for the destruction of ten million Dalek ships, but also admits that the Time Lords went with them.
In the episode "The Satan Pit", the beast calls The Doctor, "the killer of his own kind." Also, in "Utopia", the Doctor explains to Jack Harkness that if a Time Lord absorbs the time vortex, he would become like a vengeful god.
In "The Sound of Drums", the Doctor admits that he personally ended the war, in an act which caused the Time Lords, the Daleks, Gallifrey and Skaro to burn.
Although the Doctor initially believes himself to be the last survivor of the Time War, in the episode "The Parting of the Ways" he discovers that, in addition to the lone Dalek in "Dalek", the Dalek Emperor itself had also survived, and had gone on to build a whole new Dalek race, using the organic material of Human cadavers by completely rewriting their DNA. The Doctor is convinced that he himself is the only surviving Time Lord, saying that he would know of any others if they had. The destruction of the Emperor and his fleet by A declaration that "The Time War ends."
In "Doomsday" it is revealed the elite Cult of Skaro survived by fleeing into the Void between dimensions and survived the original end of the Time War, taking with them the Genesis Ark. The new Dalek army released from the Ark is eventually sucked into the Void, but the Cult of Skaro uses a "temporal shift" to escape. They reappear in New York. All but the Dalek Caan are killed, leaving Caan as the last known living Dalek.
 After The Time War
The destruction of the Time Lords creates a vacuum that may have left history itself more vulnerable to change. In the episode "The Unquiet Dead", the Doctor tells Rose that time is in flux, and history can change instantly