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The Doctor says he can't go back on his own timeline (for example, Smith and Jones, "except for cheap tricks"). It's implied it's a very bad thing to mess with his timeline.

What are the instances of the Doctor's timeline being rewritten (by his own actions or by others)?

Not instances where he doesn't remember an event in which more than one incarnation of him appears but only one may retain the full memories (like in The Five Doctors, Time Crash, The Day of the Doctor). Just instances in which he has lived through two "versions" of the same event.

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    The Time War is a big one. He destroyed Gallifrey, then went back on his own timeline and changed it so that he time-locked it instead. See here: scifi.stackexchange.com/questions/47719/… – Rand al'Thor♦ Jan 8 '16 at 16:43
  • Clara scaring the pants out of him as a child in "Listen" comes to mind. Maybe that's what caused everything. I love it. – tilley31 Jan 8 '16 at 16:53
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    @tilley31 Wouldn't this be an instance of a closed loop, instead of rewriting history? – confusedwhovian Jan 8 '16 at 17:00
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    @confusedwhovian Sometimes, with this show, I don't see the difference. – tilley31 Jan 8 '16 at 17:02
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    Ohh! Ohh! "Journey to the center of the TARDIS". I hate that episode, but The Doctor did rewrite that day, which felt like a cheap cope-out and almost made me think about quitting the show. – tilley31 Jan 8 '16 at 17:08
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Series 7: "Journey to the Center of the TARDIS"

In one of the worst stories of the Moffat era (at least in my opinion), the TARDIS gets salvaged by the Van Baalan bros, and all hell breaks loose. Even Clara learns the Doctor's real name. Then, with the "Big friendly button-ex Machina", the Doctor erases that day, and it never actually happened.

I'll add more if I find/remember them, but I feel like this is a prime example, and why the show should never do it again.

UPDATE:

Series 1: "Father's Day"

A good example of how trying to re-write history is a bad idea. Rose Tyler wants to go back in time to the day his father died. She gets all emotional, and saves his life. The reapers appear, never to be seen again. I think it was a good idea, but in the next 10 years it was never explored, nor explained again. At the end of the day, Rose's dad figured it out, and sacrificed himself so time could be stable again, so I'm not sure if it counts.

Series 4: "The Waters of Mars"

Another example of "one does not simply re-write history". The Tenth Doctor almost goes insane trying to save a crew of astronauts in Mars that had to die anyway. We get introduced to one of the most confusing concepts of New Doctor Who: Fixed points in time. Again, not sure if it counts.

As for Classic Doctor Who, I'm not very familiar with those stories, because they are so hard to find where I live. Let's wait if anybody can come up with examples of the classic era.

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  • Thanks, I had forgotten this. I agree it was an awful resolution to a very confusing story. Though I liked seeing more of the TARDIS. But there are "good" examples of rewriting history, like The Two Doctors, in which it's central to the plot. I'd like to know more examples... – confusedwhovian Jan 8 '16 at 18:09
  • @confusedwhovian I added two more examples of New Who. Not sure if there are more. Can't really discuss the classic era, because I'm not very familiar with it. – tilley31 Jan 8 '16 at 18:20
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    Isn't it a "Deus ex big-friendly-button" ? :) – Lightness Races with Monica Jan 8 '16 at 18:29
  • Tilley, two more I didn't remember. Yes I believe at least the first count, since (FD) the Doctor had been "eaten" and reappears. However (TWoM) the Doctor feels history changing, but not his personal history. @LightnessRacesinOrbit: Not always, as in "The Two Doctors", but it's worth the discussion! – confusedwhovian Jan 8 '16 at 18:29
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In the pandorica opens part 2 (season 5, episode 13), the doctor keep helping is past self and even sees himself dying, or give himself a fez...

But its in a closing time loop, so I don't know if it really counts.

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