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Throughout the new Doctor Who (2005) series, you can encounter The Doctor saying that he destroyed Gallifrey and Daleks to stop the universe from burning.

In The End of Time (2), return of Gallifrey disturbed The Doctor a lot. Reason: He didn't want the universe to burn.

In the mini episode The Night of The Doctor, the lady pilot chose to die instead of accepting The Doctor's help. It seemed like she was having bad time due to the Great Time War. Also, in the same episode, Sisterhood of Kahn persuaded The Doctor to finish the Great Time War as if they were severely affected.

In the beginning of The Day of The Doctor, it seemed like The War Doctor wanted to save the universe from burning. But, in the end, it seemed like Gallifrey was losing (Gallifrey was surrounded by Daleks and Gallifrey was only defending with little hope. They also said, "Doctor do something.") and it looked like The Doctor was acting from the side of Gallifrey, not as an authority of the burning universe.

Also, we didn't see ships of any other species in The Day of The Doctor. How was the Great Time War not a normal interplanetary war? How was it affecting the entire universe?

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Gallifrey was on the outer reaches of the time war. In the center, millions died and were reborn to die and die again.

PARTISAN: Perhaps it's time. This is only the furthest edge of the Time War. But at its heart, millions die every second, lost in bloodlust and insanity. With time itself resurrecting them, to find new ways of dying over and over again. A travesty of life. Isn't it better to end it, at last? 
RASSILON: Thank you for your opinion. 
(The Lord President stands and aims his blue metal gauntlet at the Partisan. Energy strikes her, she screams and is atomised)

The Geth from season one lost their bodies and became gaseous because of the time war. The Nestene and the Zygons lost their planets.

GELTH: Once we had a physical form like you, but then the war came.
DICKENS: War? What war?
GELTH: The Time War. The whole universe convulsed. The Time War raged. Invisible to smaller species but devastating to higher forms. Our bodies wasted away. We're trapped in this gaseous state.

At the end of the war, the Time Lord high Council wanted to implement Ultimate Sanction, destroying all of time and the universe so they can ascend.

DOCTOR: You weren't there in the final days of the War. You never saw what was born. But if the Timelock's broken, then everything's coming through. Not just the Daleks, but the Skaro Degradations, the Horde of Travesties, the Nightmare Child, the Could-have-been King with his army of Meanwhiles and Never-weres. The War turned into hell. And that's what you've opened, right above the Earth. Hell is descending.
MASTER: My kind of world.
DOCTOR: Just listen! Because even the Time Lords can't survive that.
RASSILON: We will initiate the Final Sanction. The end of time will come at my hand. The rupture will continue until it rips the Time Vortex apart.
MASTER: That's suicide.
RASSILON: We will ascend to become creatures of consciousness alone. Free of these bodies, free of time, and cause and effect, while creation itself ceases to be.

It affected the universe because of the sheer power of the time lords and Daleks, like humans with nuclear weapons affecting ants living below the battlefield.

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  • 1
    Source of third paragraph?
    – user931
    Jan 28, 2015 at 4:10
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    @Sachin again, the end of time part two PARTISAN: Perhaps it's time. This is only the furthest edge of the Time War. But at its heart, millions die every second, lost in bloodlust and insanity. With time itself resurrecting them, to find new ways of dying over and over again. A travesty of life. Isn't it better to end it, at last?  RASSILON: Thank you for your opinion.  (The Lord President stands and aims his blue metal gauntlet at the Partisan. Energy strikes her, she screams and is atomised.) 
    – user16696
    Jan 28, 2015 at 14:18
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    Russell T Davies also wrote a piece describing his vision of the Time War and its effects on the universe in Doctor Who Annual in 2006, it's quoted in full here (and here is an archived version in case the link goes dead), I think it provides some additional insight beyond the quotes from the show.
    – Hypnosifl
    Jan 28, 2015 at 22:11
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    In particular, note this paragraph: "The War raged, but for most species in the universe, life continued as normal. The War was fought in the Vortex, and beyond that, in the Ultimate Void, beyond the eyes and ears of ordinary creatures. The Lesser Species lived in ignorance. If a planet found its history subtle changing – perhaps distorting and rewriting itself under the pressures of the rupturing Vortex – then its people were part of that change, and perceived nothing to be wrong. Only the Higher Species – those further up the evolutionary ladder – saw what was happening."
    – Hypnosifl
    Jan 28, 2015 at 22:36
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    Good point, in The Unquiet Dead the Gelth said "The Time War. The whole universe convulsed. The Time War raged. Invisible to smaller species but devastating to higher forms." The paragraph from RTD's piece provides some more detail on why, though. (The idea that the war itself was fought mainly in the Time Vortex, affecting the rest of the universe by changing its history...although Night of the Doctor suggested more concrete effects on the outside universe, maybe Moffat either didn't realize RTD's conception or decided to change it, unless the human-looking Cass was a "higher species").
    – Hypnosifl
    Jan 28, 2015 at 22:54

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