That said, the episode did leave a few notable plot threads dangling and Moffat, with the help of Darvill, have released a storyboarded "deleted scene" with voiceover that details exactly what happened to "The Ponds" after their departure as well as the fate of Brian Williams, Rory's father (actor Mark Williams), still "watering the plants" in the present.
The remainder of this post contains MAJOR SPOILERS for the Doctor Who season 7 midseries finale. Any readers who have yet to see the episode and are attempting to avoid spoilers should turn away now (and do not watch the video).
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For anyone who hasn't seen the episode but wants to have context for the video epilogue (which you can view at the top of the page), in "The Angels Take Manhattan," The Doctor, Amy, Rory, and River Song encounter a weeping angels plot to farm food sources by sending victims back in time - subsequently feeding off the lingering energy over the years. However, The Doctor and friends successfully create a time paradox that shuts down the angels' battery farm - but not before a surviving angel suddenly appears and maroons Rory in 1950s New York City, aiming for Amy next.
Knowing that the wibbly wobbly timey wimey stuff caused by the paradox makes it impossible for The Doctor to return to the past to save Rory, Amy says her goodbyes and blinks, allowing the angel to send her back in time (to rendezvous with her husband). After the emotional goodbye, the episode concluded with one final scene - where the Doctor reads a letter from Amy describing what happened to the pair after they were transported back in time (they grew old together and lived a good life).
However, fans who've journeyed with the Ponds throughout the last couple years found that a few remaining plot points were unaddressed in the wake of the midseries finale, specifically: did the Ponds ever get to properly parent a child (a point of contention that was hammered in the season 7 premier) and what happens to Brian (a man that was only introduced as a supporting character this season)? The last we heard, Brian had given the pair his blessing, encouraging them to travel with the Doctor for as long as they lived - while he stayed behind to "water the plants."
Fortunately, the epilogue directly addressed the two remaining questions, providing a "happy" ending (respectively) for everyone involved - as well as offering a few more details about Amy and Rory's post time-traveling lives (example: Rory gardens). While the scene was never filmed, the Doctor Who producers released animated storyboards, complete with Arthur Darvill's voiceover, and an accompanying musical score. The resulting video, titled "P.S." would certainly have been a moving addition to the show had it actually been shot but anyone who enjoyed the Ponds, and was sad to see them go, will nevertheless still find the draft video especially moving.
In the scene, Brian is seen watering the plants at Amy and Rory's house when an older man knocks on the door and delivers a letter. The letter is from Rory - written years before his death in order to break the news to Brian that they will never see each other again as well as describe the life that Amy and Rory shared while stuck in the past. They were happy and, in 1946, adopted a son, Anthony Brian Williams, the old man who delivered the letter to Brian. The video closes with grandfather Brian and grandson Anthony hugging, presumably the start of another relationship that defies the boundaries of time and space. Basically business as usual on Doctor Who.
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Doctor Who season 7 continues in 2013 on BBC and BBC America. In the meantime, check out our Doctor Who Viewing Guide: Tips, Suggestions & Complete Episode List!