The is the second part of a two part story that started with The Rebel Flesh.
The Gangers and the humans are still in two groups, both wishing to kill the other one. The humans calls for rescue and a support ship is sent. Miranda gives the rescuers a password which the other Miranda is able to guess and redirect the rescuers to them. The Gangers want all the other gangers to rise up and take over the planet.
Rory Williams is with one of the Gangers called Jenny Lucas as they try to get back to the other group but are not having much luck. During Rory's flight, he comes across two Jennys and one kills the other. The one that is killed is a Ganger.
The two Doctors work together to work out how to resolve the situation. Amy Pond notices that both Doctors are wearing different boots and so is able to work out which is the real one and which is the Ganger.
When one of the humans is killed in a vat explosion, The Doctor persuades the Ganger version to take the place of the human for the sake of the family of the real one who has a young son.
Jenny's Ganger turns into a creature, the sort you expect from horror movies. When everything looks bleak, the Tardis drops through the ceiling and the remaining humans get into the Tardis. The Doctor Ganger and one of the other Gangers decide to stay behind to stop Jenny. The real Doctor gives the other Doctor his sonic screwdriver which kills the Jenny Lucas and then the Doctor and Miranda Ganger.
Onboard the Tardis, after dropping off the other humans, the Doctor turns on Amy and says she's a Ganger who then turns to wax and melts. The Doctor promises to find the real Amy Pond.
Amy Pond is hospital garment on a bed in a white room pregnant screaming as she's about to give birth. A slot in the wall opens and there's a woman face who looks on Amy. The same face had appeared in earlier episodes of the series.