When we last left our heroes, we met a second Doctor! Or rather a Doctor ganger… One of the side effects of getting electrocuted by the solar storm was that his DNA was transferred to the Flesh and now there’s a Doctor ganger, 100% like the real Doctor, except for his shoes. Well, he was electrocuted before his shoes were damaged by the corrosive stuff on the island and changed his shoes. Amy points this out, by the way, then proceeds to tell him that she definitely knows which Doctor is which. There’s a couple of long conversations about this during the episode in which Amy concludes that she can’t trust the ganger Doctor.
Anyway, most of the crew plus Doctor ganger go off to find Rory, who was looking for Jennifer. In the meantime, the gangers have all come together to discuss their plans for killing the humans. Well, ganger Cleaves doesn’t like the idea (as she’s dying from the same disease as her human), but she’s convinced by ganger Jennifer to kill them all. She goes off and finds real Jennifer and kills her, then stages a fight with another ganger in front of Rory to convince him she’s the real Jennifer (we know she’s dead, but he doesn’t). Oh, and she uses Rory to get all the humans inside a room where the gangers try to kill them all with the corrosive liquid. One of the crew, Jimmy, ends up dying, so the ganger Doctor finds his way to the gangers to talk to them.
At first it seems as though he’s trying to work with them, on their side, but we know the Doctor, even if he is a ganger… Anyway, a hologram call comes in during this all and it’s Jimmy’s son. He just died, but his ganger is there and has all the same emotions built in. Everyone’s convinced that they shouldn’t kill their humans except Jennifer, who runs off. They free the humans and everyone runs toward the TARDIS, except Jennifer, who’s become a monster. They get to the TARIDS on time and ganger Cleaves offers to hold open the door, even though it’ll kill her. The Doctor that Amy’s been hanging with joins her, showing that he’s the ganger Doctor – he switched shoes a long time ago and Amy gives him a teary apology.
Anyway, the Doctor turns this ragtag group of gangers into full-fledged humans and cures Cleaves before dropping them off at Flesh headquarters. They’re going to tell everyone the truth of what happens with the gangers.
Then when they all get back in the TARDIS, Amy starts having contractions and the Doctor reveals that he intended to bring them to the monastery to investigate just how lifelike the Flesh can be. Because this Amy is not actually Amy at all – she’s a ganger, and she’s been a ganger for quite some time. And the Eye Patch Lady she’s been seeing randomly has her body on a spaceship somewhere, incubating the pregnancy. Finally, Amy wakes up in this white bubble 100% pregnant and the Eye Patch Lady tells her she’s ready to pop. Scariest I Didn’t Know I Was Pregnant episode ever? Next time will have 100% more baby.