Rory, The Doctor and Amy

In the TARDIS, The Doctor is once again covertly scanning his travelling companion Amy Pond to determine if she is pregnant or not. But the TARDIS is still showing The Doctor inconclusive readings. As The Doctor tries to work out what is wrong with the scanner the TARDIS gets hit by a solar tsunami, and ends up materialising near a monastery on a remote island in the 22nd Century.

As they explore their surroundings The Doctor notices a pipe half buried in the ground, and deduces that it is pumping a highly corrosive acid to the mainland. As they enter the monastery they set off an alarm. They then enter a room full of harnesses in which people are sleeping. Alerted by the alarm the room suddenly contains exact doubles of the people in the harnesses. The Doctor pretends to be from the meteorological department and warns them that a bigger solar wave, than the one they just survived, is on the way. Miranda Cleaves (apparently the leader) leads them to a room containing a vat of ‘Flesh’; fully programmable matter which they can manipulate to replicate any living organisms. They reveal that all the workers in the room (apart from Jennifer) are created from Flesh and are known as ‘Gangers’. They also reveal that they are being controlled by the real people in the harnesses. As Jennifer leaves, to create her Ganger, The Doctor scans the Flesh, but instead feels it scanning him. As Jennifer steps into the harness, The Doctor, Amy and Rory watch Flesh pour into a tub. The liquid Flesh then reveals an exact copy of Jennifer.

The Doctor reminds them of the solar wave, but Cleaves refuses to let the team leave the island. The Doctor notes that the factory runs on solar energy, meaning there will be a huge power surge when the wave hits. Jennifer directs them to the monitoring station where The Doctor sees that solar energy is absorbed via a weather vane, and heads up to the roof. As the power surge occurs, acid pipes begin to leak everywhere, including near the TARDIS which begins dissolving the ground around it, and the Gangers switch between their full human forms and their semi-Flesh forms. The blast from the solar energy also knocks The Doctor back from the weather vane. When he wakes up, on the roof, he sees that the weather vane gone. The Doctor locates the real Cleaves, who is deeply shaken and worried for her team. The Doctor reveals that they’ve been unconscious for an hour, rather than a few minutes as Cleaves believed. After also being knocked unconscious Amy and Rory return to the harness room to find everyone awake. Jennifer apparently is in a state of shock and so Rory comforts her. Cleaves announces that the Gangers should have returned to pure Flesh, but it seems she is wrong as it discovered that the Gangers are controlling themselves. The Doctor also explains that the Gangers are searching for confirmation of their identities as the process of creating the Gangers has meant that they have given their identities away. The workers though have trouble accepting this.

Rory and Amy Exploring

Amy then remembers Rory, who had earlier left the room when Jennifer had begun feeling ill, and so she goes to search for him. With Jimmy and The Doctor, Any arrives at the toilets but there is no sign of Rory or Jennifer. But The Doctor realises from a piece of discarded Flesh that Jennifer is a Ganger. The Doctor also deduces that though the Gangers are not violent they are scared and that he needs to talk to them if he is going to fix things. The Doctor heads off to get the TARDIS while Amy continues to search for Rory. On his way to the TARDIS, The Doctor returns to the vat of Flesh and scans it with his sonic screwdriver again before leaving. The Doctor though is unaware that after he has left the tub fills with Flesh again, and drains enough to reveal a pair of lips. The Doctor returns to where he left the TARDIS to find only the top part remaining above ground. He also realises that the ground is saturated in acid and that it has burnt his shoes. Meanwhile, all the Gangers except for Jennifer have gathered with the remaining acid suits.

While searching for Rory, Amy briefly sees the Eye Patch Lady again. She is soon joined by Rory, Ganger Jennifer, Buzzer and Dicken. The group return to the main room with Jimmy, and The Doctor soon arrives with the rest of the Gangers in full human form. He explains that the Gangers are now truly alive. The real Cleaves enters but she refuses to work with the Gangers, and kills Ganger Buzzer. The Gangers conclude that the humans can not be trusted and so run out. Cleaves tells the humans that it is war, as does the Ganger Jennifer to the Gangers and so the Gangers, in acid-protection suits then bear down on the humans forcing them to take refuge in the chapel. Rory though takes off to try and find Jennifer, and so is separated from the group of humans. After the door is barricaded The Doctor hears a voice and tells whoever is in the room to show themselves. A human figure emerges from the shadows. It is a Ganger of The Doctor and it is heard saying ‘Trust me, I'm The Doctor’.

Amy and the Humans/Gangers

The Ganger Doctor finalises his shape and eventually stabilises after finding it difficult to cope with The Doctor’s past regenerations. Amy is initially horrified but The Doctor and the Ganger Doctor quickly take a liking to each other. Furthermore, unlike the other Gangers, the Ganger Doctor appears to be more friendly towards the others. With the help of both Doctors, the group find an escape route out of the chapel and they make their way to the control room, where it is established that the ‘real’ Doctor, having changed shoes since coming into contact with the acid, can be distinguished from the Ganger Doctor. However, both Doctors maintain that they are as good as equal, which both Amy and Cleaves find difficult to believe despite the two Doctors continually completing each other’s sentences. It is then that Cleaves makes the decision to evacuate, leaving The Gangers behind, and to burn the acid factory down.

Rory, meanwhile, has tracked Jennifer down after her flight, but he finds that there is also another Jennifer. At first he cannot distinguish between the two of them but eventually realises that one is limping. The intact Jennifer attacks the injured one, which culminates in the ‘real’ Jennifer throwing her Ganger into a puddle of acid. Meanwhile the Gangers contemplate what to do while the real Cleaves sends a transmission to the mainland to request immediate evacuation. The Doctors realises that before they head to the evacuation tower, Rory and Jennifer should be tracked down. The real Doctor finds out that he can track them by using his sonic screwdriver, since Gangers and humans cause a slightly different response from the tool. Buzzer and the Ganger Doctor are sent to track down Rory and Jennifer. They soon find Jennifer, who is lying in the courtyard, but she dies just as they arrive. Buzzer then incapacitates the Ganger Doctor, on Cleaves’ orders.

Rory, unaware that the Jennifer he is with is not the ‘real’ Jennifer but another Ganger, enters a thermostatic control room, where Jennifer uses Rory to shut off the thermostatic regulators. In the control room, Cleaves realises that the coolant systems are offline and announces that this will eventually cause the facility to explode. Even though they do not know how much time is left, the group heads to the acid storage room to try and prevent the cataclysmic reaction caused by the boiling acid. There, The Doctor finds that the chemical reaction has already started and cannot be stopped. Jennifer locks the group in, and Rory announces that he has seen what happens to the old Gangers, and wants to stop it. However, Amy and The Doctor point out that Jennifer is dead and that he has been tricked into following a second Ganger of Jennifer. Realising his mistake Rory is taken back to the chapel, by Jennifer, where they are joined by the remaining Gangers including the recovered Ganger Doctor.

The Gangers in Protection Suits

After receiving a video link, from Jimmy’s son, the Ganger Jimmy flees, unable to face ‘his son’. Ganger Jennifer - who has been trying to enlist the other Gangers into a revenge mission - flees, believing that the Ganger Doctor has made Ganger Jimmy weak. Ganger Jimmy, realising that the humans and the Gangers can get along, heads for the acid containment room but when he enters the room he is just in time to see the real Jimmy get hit in the chest by some spitting acid. As he dies Jimmy asks his Ganger to answer his son’s call. The Doctor and the remainder of the group then head to the chapel, where Ganger Jimmy answers his son’s call.

Rory then announces that he has found an escape route under the crypt and the two Doctors realise that the passage leads to just under where the TARDIS has been sinking. They all head along the passage, where they are greeted by the TARDIS falling through the ceiling. But they are also being pursued by Ganger Jennifer, who has now become a scorpion-like creature. Unable to lock the door, Ganger Cleaves and The Doctor are left holding it shut, separating Jennifer from the group. Amy, having become increasingly hostile towards the Ganger Doctor, tries to get The Doctor to swap places with the Ganger Doctor and come into the TARDIS. It is then revealed that the Ganger Doctor and the ‘real’ Doctor had swapped places to allow the ‘real’ Doctor to infiltrate the Gangers. Therefore, what Amy thought was the Ganger Doctor was in fact the real Doctor and so The Doctor holding the door shut is the Ganger. Amy at first does not believe The Doctors, but when it is revealed that they swapped shoes, Amy and Cleaves realise that The Doctor’s point had been proven and that the two races can get along after all. The Doctor gives his Ganger the sonic screwdriver, and takes Amy, Rory, Buzzer, Ganger Jimmy, Cleaves and Ganger Dicken into the TARDIS which then dematerialises. The Ganger Doctor then opens the door and uses the sonic screwdriver on Ganger Jennifer causing her to collapse back into raw Flesh. But the sonic disturbance also has the same effect on the Ganger Doctor and Ganger Cleaves who also collapse back into raw Flesh.

After dropping off Ganger Jimmy, to be ‘reunited’ with his son, and Cleaves and Ganger Dicken, at a press conference being held on the incident, The Doctor, Amy and Rory head back towards the TARDIS. But when Amy doubles up in pain The Doctor says she is contracting, and about to give birth. But Amy insists that she is not pregnant. However, back in the TARDIS, The Doctor tells Rory to step away from Amy. At first Rory refuses but eventually, and reluctantly, he backs away from Amy. The Doctor then tells her to hold on and that they will find her. A confused Amy protests that she is right here. But when The Doctor grimly replies that she is not, and she hasn’t been for a long time, he points his sonic screwdriver at Amy and activates it causing her to collapse into raw Flesh.

Amy wakes up in a hospital gown and on a metallic table. A panel in the wall slides away, and the Eye Patch Lady, whom the Ganger version of Amy had been seeing occasionally during her recent travels with The Doctor, announces that she is ready. Amy looks down and discovers that she is very heavily pregnant. As her contractions begin, the mysterious woman tells Amy to push and Amy screams in horror...