When we last left the Doctor, Amy and Rory had rejoined him as his full-time traveling companions. Unfortunately, things are about to take a turn for the worst.
As you might expect from the title, "The Angels Take Manhattan" features the return of the Doctor's most infamous enemy. The Doctor discovers a strange book about a character named Melody Malone (Melody is the birth name of River Song). Soon after, Rory is nabbed by a Weeping Angel, and sent back to 1938. He meets up with River Song, who turns out to be the author of the book the Doctor is reading in the future.
The Doctor and Amy use the book to travel to 1938 New York, an area of space-time they discover to be particularly difficult to travel to. The Doctor then discovers that the last chapter in the book is titled, "Amelia's Farewell," and becomes obsessed with trying to change future events. After a disturbing run in with miniature "cherub" Angels, the Doctor, River, Rory, and Amy reunite, and investigate the Winter Quay hotel. There they discover that the Angels have concocted a macabre arrangement. They kidnap people, trap them in the hotel, then constantly feed off of their energy by keeping them in an endless time loop. To escape this fate, Amy and Rory jump off the roof to create a paradox, erasing the Angels and the hotel.
However, just as they are celebrating their victory, a surviving Angel grabs Rory and transports him back in time again. The Doctor explains that rescuing him would cause another paradox that would rip time and space apart. Despite the Doctor begging her to come with him, Amy instead tells him goodbye, and allows the Angel to transport her back as well. This creates a fixed point in time, and means that the Doctor will never be able to see them again.
As if this episode wasn't heartbreaking enough, it ends with the Doctor discovering the epilogue in the Melody Malone novel, written by Amy who is now living in 1930s New York. She tells him that she and Rory are well, and that the Doctor should find new companions, as he should not be alone. She ends by asking him to visit a young Amy Pond as she waits for him in her garden.
Despite how you feel about the Ponds, it's hard to deny that this was probably the biggest loss for the Doctor since Rose. At least with Rose, her and a version of the Doctor got to live happily ever after.
"Angels" was followed by "The Snowmen," the 2012 Christmas special. The aftermath of "Angels" has left the Doctor in mourning, hiding away in Victorian London. Unfortunately, the Doctor soon finds that a creature called the "Great Intelligence," appearing as snow, has been plotting to create an army of evil snowmen. In a strange twist, the Doctor also meets a girl named Clara, who turns out to be none other than Oswin Oswald (the Dalek girl from "Asylum").
The two join forces and defeat the snowmen, but not before Clara is killed after falling from a cloud. However, the Doctor is able to deduce that a person dying twice is impossible, and that Clara must be alive in some other time and place. The Doctor, reenergized and reinvigorated, departs to find her. As it turns out, she is alive and well, as we see her visiting her own grave in modern times.
This will hopefully lead into the next episode of the season, titled "The Bells of Saint John."