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There are always milestones and momentous episodes in "Doctor Who" - stories which are described as "the one where Sarah-Jane leaves", "the one where Adric dies" etc. It's taken a while for one of these types of stories to happen in the Eleventh Doctor era and they definitely pull out all the stops. Let me ask a question. Do you watch "The Hand of Fear" and pick at plot holes? Of course not. You watch it with emotion not logic and eat up all the scenes with Sarah-Jane and the Doctor, knowing it's their last ones. It should be the same with "The Angels Take Manhattan". You cannot watch this dispassionately. You cannot deliberately turn off your emotions and watch this from a logical standpoint. As Matt Smith said: "Never apply logic to Who". This was the swansong of two beloved characters - the only family that Eleven has known - and it was glorious.
This wasn't a story cluttered with an incomprehensible plot or multiple, unnecessary characters. In fact, the plot itself was relatively straightforward but I'm not going to recap it because of two reasons: firstly. it's not hugely vital and secondly you need to watch this story yourselves. Basically, it was a lovely, typically Moffat story where Time is important and full focus is given to those characters we've grown to know and love: The Doctor, River, Amy and Rory. The relationships between them came to the forefront - we'd seen the bond between the Doctor, Amy and Rory in "The Power of Three" and in "The Angels Take Manhattan" we saw the strength of the bonds between Amy and Rory, Amy and River, River and the Doctor and, of course, Amy and her "raggedy man".
It really was a beautiful end to the Pond era - and, whilst we were promised tragedy, we did slightly misunderstand what that meant. We all took it to mean a tragic end for the Ponds...but was it? Amy and Rory wanted and needed to be together - and that's what they got. They grew old together - and if you cast your minds back to last year's "The Girl Who Waited", that's what Rory wanted more than anything and, in this story, that's what Amy chose. Choices were important here - Rory chose to jump off the building and create a paradox. Amy chose to join him - "together or not at all". It was a truly superb scene that really highlighted the strength, love and connection that Amy and Rory have. We had hope then - hope that was cruelly ripped away by the graveyard scene. Another choice. Amy chose to be with Rory. Wherever Rory was, that was home to Amy. Her "raggedy man" was her friend...but Rory was her life. They were together - the tragedy would have been if they weren't.