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In the two parter in the 5th season of Doctor Who (the new series), made up of The Pandorica Opens and The Big Bang, the Universe is "rebooted" and Amy seems to be significant in this process. When she wakes up, it's the morning after she originally left with the Doctor and it's her wedding morning. She has parents now, when they weren't present before the Universe was rebooted. Also, at this point, until she remembers him, the Doctor doesn't exist.

Are there other differences between the rebooted Universe and the original one?

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Amy's parents (Augustus and Tabetha) were originally lost (wiped from history) because they came into contact with the crack in Amy's wall (revealed in "The Big Bang", but hinted at earlier); Rory was also lost in this way (at the end of "Cold Blood"). They were restored because the Doctor sealed himself (and the TARDIS) on the "other side" of the cracks, which mean that he was wiped from existence.

Because the Doctor never existed, the TARDIS never (timey wimey) exploded, and the cracks didn't appear, so she never lost her parents or Rory. Presumably all the other losses to the cracks (e.g. Father Octavian's soldiers and the Weeping Angels from "Flesh and Stone") were also undone.

Possibly other adventures of the Doctor were wiped as well (although Earth had somehow survived to the 21st Century), although if so these were apparently (since they are referred to later) restored when the Doctor is restored.

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