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At the end, the doctor steps into the crack and is erased from history completely.

This means that he was never there to save the earth. For example, he never stopped the reality bomb (4th season) and he never stopped the time lords from destroying the time vortex during the time wars.

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Everything the Doctor did in his life still happened even after he was erased. Even though the cracks erase things from history, they don't erase the effects of those things' existence. We've seen this a number of times before in instances concerning the cracks:

  • Even though the Weeping Angels were erased, the Byzantium still crashed.
  • Even though the cleric who gave Amy her communicator was erased, she still had the communicator.
  • Even though Amy's parents were erased, she still existed.
  • Even though Rory was erased, his ring was still on the TARDIS and there was still a photograph of him in Amy's house.
  • Even though the Doctor was erased, Amy still had dolls and pictures of him on her desk.

As you can see, these are paradoxes. However, that is what the cracks do - they rip things out of causality but don't account for any of the changes that doing so would normally cause, so they generate all kinds of contradictory situations that don't make any sense from a logical standpoint. People in the show never notice this because the cracks also affect one's memory and, it seems, their perception as well to a certain degree, as the cleric from "Flesh and Stone" and Amy herself insisted that his fellow clerics and her parents, respectively, had either never been there to begin with or had been "lost." However, the Doctor notices, and that is why he says that he life doesn't make any sense - it's missing a bunch of important chunks, but it still happened even though she herself should no longer exist. It's the same way with the Doctor once he is erased. He may be gone, but his "footprint" on the universe (saving worlds, defeating enemies) is still there, and until Amy remembers him back into existence, it doesn't make sense (but nobody notices because they were made not to think about it by the erasure itself).

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  • Of course, this doesn't resolve the paradox of Amy being able to 'remember' the doctor back into existence. It raises the question of why she couldn't do that with Rory. – ardent Jun 20 '13 at 0:39
  • She did remember Rory back into existence; that's why he was even at the wedding in the first place. We see her remembering him in "The Pandorica Opens". It just so happened that his consciousness was already integrated into a Nestene duplicate at the time that she remembered him, and his human self wouldn't have been born for another 2000-ish years, so it's not like he would have just materialized in 102 A.D. – Amy Jun 20 '13 at 4:50
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    The doctor also explains this by stating something to the effect of "The whole universe seeping into your head [from the crack in her wall]" Which is implied that this gives her the ability to remember things that others could not. – Arammil Jul 12 '13 at 11:00

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