At the end of ‘The Angels Take Manhattan’ the Doctor tells Amy that he will never be able to see Rory and her again. Some have speculated that this might not be true and that we may have already seen the Doctor visiting the Ponds in their past. That the preceding episodes occur out of order from the Doctor’s perspective.
This idea isn’t without precedent. River Song introduced the idea of the Doctor meeting a companion out of order. In that specific case these meetings weren’t the Doctor’s choice. Similarly the Doctor crossed his own time line briefly to speak with Amy in ‘Time of the Angels’ but that to wasn’t his choice and more a happy consequence of the crack in times healing.
‘The Impossible Astronaut’ showed the Doctor visiting earlier versions of Amy and Rory, reuniting with them before his death. ‘The Wedding of River Song’ brings us back to this moment, the future Doctor now our present Doctor. This is again a special situation. The Doctor arranges this reunion because he has to ensure that he meets the criteria of the fixed point in time.
The 2nd Doctor speaks of bending the rules to visit the Brigadier in ‘The Five Doctors.’ In this case it is because he is visiting a companion after they’ve encountered his 3rd and 4th incarnations. None the less this does suggest that the Doctor has a desire to visit past companions, even if the laws of time say he shouldn’t.
The idea that the Doctor would visit Amy and Rory before their fateful trip to Manhattan is part of the wish fulfilment of time travel. The Doctor never has to say goodbye when he has the TARDIS.
Past incarnations of the Doctor have had the excuse of poor piloting to explain why they don’t regularly revisit departed companions. ‘School Reunion’ also suggests that the Doctor can’t bear to see his friends age and wither.
The Doctor’s reverence for a fixed timeline coupled with his inaccurate landings shows why the Doctor didn’t try to visit his old friends. He couldn’t guarantee how old they would be when they met and if they said this was the first time they’d seen the Doctor since they went their separate ways then he’d never be able to see them when they were younger.
The 11th Doctor has much more accuracy and is shown visiting the Ponds in ‘The Doctor, The Widow and the Wardrobe’ and is making plans to do so again in ‘Pond Life’. So he certainly has the capability to revisit them.
If there is a gap between ‘The Power of Three’ and ‘The Angels Take Manhattan’ then the 11th Doctor could have lost the Pond and then had the episodes of the previous episodes.
I would suggest that in ‘Asylum of the Daleks’ the Doctor and Ponds were taken from the same relative time period. Even the Doctor believes that the Daleks won’t deliberately damage time and so could be counted on not to create a paradox. In addition the Doctor is more concerned with the break up of their marriage than he is with their potential deaths destroying New York.
This all points to this adventure taking place before ‘The Angels Take Manhattan’ from the Doctor’s perspective.
A better candidate is ‘Dinosaurs on a Spaceship’. If this is set after ‘The Angels Take Manhattan’ the Doctor having new companions in the form of Riddell and Nefertiti is his attempt to follow Amy’s wish for him not to be alone.
Many moments in that episode are actually improved in this interpretation. When Amy mentions the increasing gaps in time when they hear from the Doctor his reaction is that of finding out that he won’t be able to visit them at an earlier point.
His defensiveness when Amy asks him if Riddell and Nefertiti are replacements comes from his sadness that he will loose the Ponds soon and his desire for Amy not to find out the reason why he has new travelling companions. This is reinforced by the Doctor telling her that his new companions will never take the place of Amy and Rory.
There are two sticking points for this interpretation to work. Firstly putting the Ponds in danger could still trigger the destruction of New York, so it doesn’t seem likely that the Doctor would take them on an unknown spaceship.
It would also seem clear that the Doctor meets Brian Williams for the first time here and recognises him again in ‘The Power of Three’. With the release of the bonus epilogue ‘P.S.’ it seems increasingly likely that ‘The Angels Take Manhattan’ that Ponds travel with him from the penultimate episode to the last without them parting company.
Still, there is a slim possibility that the Doctor was pretending to know Brian when they first met in ‘The Power of Three’ or had indeed met him at Amy and Rory’s wedding. Brian being whisked away in ‘Dinosaurs on a Spaceship’ was entirely deliberate. He wanted to spend time with Brian and ensure that events proceeded as the situation in ‘The Power of Three’ occurred.
I like the idea that ‘A Town Called Mercy’ takes place during their month long trip during the party in ‘The Power of Three’. The glimpse of the Doctor and the Ponds hiding from Henry the 8th in the latter fits the throwaway mention in the former.
It may be revealed that the Doctor did experience these adventures out of order but I don’t think it fits the conclusion of ‘The Angels Take Manhattan’. The message is that the Doctor has to move on with his life, after giving little Amelia Pond hope.
The idea that the Doctor then kept visiting the Ponds in the past doesn’t fit thematically. The Doctor has always been about moving forward, no matter how painful that might be. He is an explorer at heart (both of them) and is more likely to forge a new future than cling to a dead past.
Still, it is a nice idea and adds to the mythical nature of the Doctor, his days like crazy paving.