The Doctor has regenerated again, and is once again having the usual post-regeneration nuttiness. He’s gone a bit weird piloting the TARDIS, and has managed to bring a Tyrannosaur into the Victorian era with him, as he reunites with the Paternoster gang-Madame Vestra, Jenny and Strax.
Eventually the Doctor manages to get some rest, although the Dinosaur is still loose. Clara isn’t particularly pleased with this new incarnation-he appears somewhat older and not nearly as personable, even though his regeneration has not settled yet.
However, the Doctor escapes from his bed, in time to witness the T-rex burst into flames…and this wasn’t spontaneous. He seems to spot a vital clue-a “half faced” man who seems to have clockwork components.
The Doctor and Clara both rendezvous at a restaurant, having been sent a newspaper ad telling them to meet up, although neither of them sent it. They discover that the people in the restaurant are not real, but are in fact, patchwork cyborgs similar to the clockwork robots the Doctor encountered in his tenth life.
Descending to the basement, he discovers that the robots are using tissue from various humans and other creatures to restructure themselves and build a ship, to go to something called “The promised Land” or heaven. However, the Doctor seems to abandon Clara as he escapes, but he soon arrives with the Calvary, with Jenny, Strax, and Vestra armed with swords to rescue her.
It ends with the Doctor fighting the half faced man, who is then impaled on a spire-but it’s unclear whether he did it himself or the Doctor pushed him.
As the story ends, the Doctor unveils a new costume-not too much unlike his Third incarnation-and takes Clara back to the twenty-first century, where he states she can leave if she’s uncomfortable with new, harsher persona and look.
However, Clara gets an unexpected phone call-from the Doctor’s former incarnation on Trenzalore, moments before his regeneration, asking her to please give the “new” him a chance. She then hugs the ‘current’ Doctor, although he’s not really the hugging sort.
Meanwhile, the half-faced man awakens in a strange garden, with an eccentric woman in Victorian clothing. She calls herself Missy, has stated that he’s made it to the promised land/heaven, and that the Doctor is her boyfriend….