Three workers (Jennifer, Buzzer, and Jimmy) a small chamber containing a circular vat filled with acid. All three are wearing heavy duty acid suits and visors. Jennifer takes an acid reading and is worried by the low result. Buzzer, standing on the rim of the vat, teases her and she accidentally pushes him into the vat. His body, and the suit, are dissolved by the acid. The other two leave to write up a report about the accident though they seem more concerned about the loss of the suit. Buzzer enters the corridor and confronts them, albeit with some jocularity, about accidents in the workplace. His body, it seems, is still melting in the vat of acid.

Amy and Rory are playing darts in the TARDIS while the Doctor surreptitiously scans Amy for pregnancy (again getting both positive and negative readings. ) he offers to drop them off for fish and chips while he goes off to deal with something else, but Amy says she would rather stay with the Doctor. The TARDIS is hit by a solar tsunami and plunges down toward Earth. It lands on an island in the 22nd century outside a medieval monastery. Amy assumes they are in the 13th century but Rory points out the Dusty Springfield song playing inside and suggests that the date is somewhat later. As they approach the monastery they see a pipe sending acid to the mainland. They pass into the building and set an alarm off. The Doctor says that they are about to be greeted by 'almost' people.

They run into a chamber where there are four bodies in harnesses (and an empty harness). Five people follow them in, four of whom are duplicates of those in the harnesses. The Doctor uses his psychic paper to show that he is from the Meteorological Department, sent on account of the solar storms. He says that an even larger storm is on the way. The foreman, Miranda Cleaves, is phlegmatic about this but the Doctor demands to be shown the "critical system."

Cleaves takes them to a vat containing the Flesh. She explains that it is biological material which can replicate living organisms. Apart from Jennifer, the workers in the room are all Flesh doppelgangers (or "gangers,") who are currently being controlled by their apparently sleeping originals from the harnesses. Cleaves tells them that the site was losing workers every week so the army started to use gangers. The Doctor scans the Flesh with the sonic screwdriver and reaches out to touch it. He says that it seems to be scanning him and is far more alive than they realise. Jennifer goes to her harness and everyone watches as a ganger Jennifer is created. The Doctor reminds the workers of the impending solar flare and some are worried but Cleaves says that they should keep producing acid until the mainland tells them to stop: difficult as the last flare knocked out all of the communications systems.

The Doctor tells Amy and Rory that the factory runs on solar power. He says that when the solar flare arrives there will be a dangerous power surge. He heads up to the roof to disconnect the weathervane that collects the power. Before he goes he tells Amy to "breathe", much to her puzzlement. He climbs a ladder and begins pulling wires from their sockets. He is still doing this when a massive solar wave hits and he is thrown from the ladder and knocked unconscious. The acid pipes burst and leak everywhere, forming puddles within the monastery and even causing the TARDIS to sink below ground. The gangers scream and start to revert back to Flesh.

The Doctor wakes up and sees that the weathervane has gone leaving only a burning base. He finds Cleaves who is no longer in her harness and showing concern for abandoning her team. The Doctor asks Cleaves how long they were unconscious for. She says a few minutes but he thinks that it has been at least an hour. Amy and Rory wake up too and return to the harness chamber. The rest of the team are badly shaken after the power surge, Jennifer is in shock and Rory comforts her. The Doctor and Cleaves arrive and Cleaves says that their gangers should have returned to Flesh forms. This is contradicted when they hear the Dusty Springfield song again: someone is playing the record in the recreation area. The gangers seem to have become autonomous. The Doctor hints that the gangers will have memories and personalities now.

The group go to the recreation room; one of the gangers has made a tower of cards and Buzzer says that this is something his grandfather taught him. The Doctor points out that the gangers have a heedful of memories now. Jennifer says she feels ill and goes to the washroom. She is followed by Rory who tells her that people should not go off alone. Jennifer vomits up Flesh into the sink. She realises that she is a ganger and goes into one of the toilet cubicles. As Rory sees the Flesh in the sink, Jennifer's arm punches out at him from the cubicle. Her head extends through the hole in the door on an enormously long neck. She shouts, "Let us live!" Rory flees.

The Doctor asks Jimmy if he is a violent man. Jimmy says he isn't and the Doctor explains that it is likely this is true for his ganger also. The Doctor passes Cleaves a plate of food. She takes it but when he warns her that it is hot she drops it. She worries that she didn't feel the heat earlier but the Doctor explains that her nerve endings aren't stable yet. Cleaves turns to her Flesh form but the Doctor tries to console her, saying that Flesh is in its early stages and the problems can be solved. She shouts at him and runs out. The Doctor says that Jennifer is a ganger, too and he and Amy to go off to find Rory, accompanied by Jimmy. The Doctor repeats that the gangers are unlikely to be violent, more likely to be scared and angry. He says that he needs to talk to them to rectify matters. They walk through the monastery corridors but their route is blocked by acid puddles. The Doctor decides to fetch the TARDIS and Amy goes to search for Rory. Jimmy makes his way back to the dining hall and orders Buzzer and Dicken to fetch acid suits.

Rory has seen Jennifer's ganger looking for him. At first he hides from her but then they meet in the locker room where she declares that she is Jennifer Lucas, not a "factory part". She says that she has memories and becomes full human, saying she is just as real as the original Jennifer. Rory embraces her as she breaks down in tears.

The Doctor returns to the vat of Flesh and scans it with his sonic screwdriver. After he leaves a mouth forms in the liquid and says, "Trust me," as the Doctor had said to Cleaves's ganger. The Doctor finds his TARDIS almost completely sunk below ground. At the same time, acid burns through his shoes. He pulls them off and goes back to the monastery in his socks. The gangers, minus Jennifer, meet up in the acid room. They have the acid suits and Cleaves says that they have the advantage now.

Amy pushes open a door and sees the eyepatch woman again, looking at her through a hole in the wall. She turns to see Rory and Jennifer's ganger who are followed in by Buzzer and Dicken. Amy tells them that this is her ganger. Rory says that no one will touch her. They go back to the dining room where Jimmy, Buzzer, and Dicken ask Jennifer's ganger about what she has done to the original Jennifer. Amy thinks that they should wait until the Doctor arrives.

The Doctor has, in fact, gone to the acid room and talked to the gangers. He tells them to meet their originals and work with them. They go to the dining room. On the way they pass Cleaves, who watches them pass with mistrust. The Doctor first asks if anyone can lend him a pair of shoes and then tries to explain that the gangers are real living people. Jimmy and his ganger share memories of his/ their son's birth. They both decide to go and find Jennifer and Cleaves together. Before they can, however, Cleaves enters the room with an electric circuit probe, capable of delivering 40,000 volts (enough to kill human or ganger). She electrocutes Buzzer's ganger when he tries to take the probe away from her. The Doctor angrily explains that Buzzer's ganger had a human heart. Jennifer decides that humans can't be trusted so Cleaves turns on her with the probe. Rory takes the probe from her and the gangers run off. The Doctor berates Cleaves but she says that it is "us or them." This is repeated by Buzzer and Jimmy. Elsewhere, the ganger Jennifer is saying to the other gangers that it is "us or them."

The Doctor asks which room is the monastery's most defendable. Cleaves tells him it is the chapel, which contains the Flesh vat. Rory goes off in search of Jennifer. The other gangers, apart from Jennifer who is hunting her "spare", march to the chapel. The Doctor and the humans lock and barricade the door. Jimmy says that it is insane; they are fighting themselves. The Doctor says that it is about to get "insanerer" as his ganger steps out of the shadows, saying, "Trust me. I'm the Doctor."

The ganger Doctor struggles to cope with its transformation, speaking as the First, Third, Fourth and Tenth Doctors while the Doctor tries to calm him down. He asks the ganger a few questions to see whether it is really him. As they do this, smoke begins to creep in at the door as the gangers try to force entry with acid. The two Doctors realise that they can tell what the other is thinking and come up with a plan to escape through an air-duct. Again, the Doctor tells Amy to "breathe." They escape down the vent as the gangers arrive in the room. They find the corridors full of choking gas - caused by the acid reacting with stone - and make their way up to the evac tower. They plan to call the mainland for help and then trace Rory and Jennifer. The ganger Cleaves knows where they have gone because she, too, is thinking like her original. Both Jimmy and his ganger pause at the chime of midnight to wish their son, Adam, a happy fifth birthday. The ganger Jen arrives, saying that she has managed to overcome the memory suppressing protocols and can remember her previous deaths. She says that the eyes are the last thing to melt. She demands that they start a revolution but Cleaves says that she wants a quiet life and to be left alone. The ganger Cleaves is suffering from bad headaches.

In the evac tower, Amy watches the two Doctors working as one, finishing each other's sentences, but says that she can tell one is the Doctor and the other is only 'almost' the Doctor. The Doctors get power into the machines and start to scan for Rory. Cleaves calls the mainland and asks for an emergency pick up from the roof of the tower. She also warns that the gangers are running amok and need to be decommissioned. Gangers Cleaves, Dicken, and Jimmy go to the control room and listen to Cleaves's transmission. Cleaves types a password and explains that this must be used in all future transmissions to the mainland. Ganger Cleaves praises her other self, saying how clever she is. Ganger Jennifer tries to access the thermal control but the palm-reader does not recognise her, displaying a message that calls her 'non-human'.

When the woman with the eye patch appears again Amy finally tells the Doctor. He tells her it is a "time mirage." The Doctor ganger leaves the room saying that "it' is in his head. Amy follows to apologise for being so unfriendly and hinting that she has seen his death. He violently shoves her up against the wall and asks "Why?"because this is what the gangers say when they must die. Inside the room, the other Doctor also says "Why?" Shaken, Amy returns to the room while the two Doctors say that they seem to be in contact with the Flesh and say that it wants revenge. The humans demand that the ganger Doctor sits apart from them on a barrel in the middle of the room.

Rory finds both Jennifers in the same room. They both argue that they are the real Jennifer, despite Rory saying that he agrees with the Doctor that both must be saved. The two girls fight and one falls into a puddle of acid and dissolves: she is a ganger. Rory and Jennifer make it to the thermostatic control room and Jennifer asks for Rory's help in clearing the deadly gas caused by the acid. Jennifer uses Rory to shut off the thermostatic regulators. In the tower, the computer notes a rise in temperature because Rory and Jennifer have shut off the cooling vents. This will boil the acid and destroy the monastery in less than an hour.

Buzzer sees Rory and Jen on a CCTV monitor and sets off to get them to the tower. The Doctor throws his screwdriver to his other self and sends him along, too. He asks Amy to trust him on this one. The Doctor's ganger and Buzzer find a dying body. The Doctor says that his screwdriver can tell the difference between human and ganger and this is the real Jennifer. She dies as they reach her. Buzzer knocks the Doctor unconscious and says that it is on the boss's orders. On his way back, he finds Ganger Jen comforting a pile of discarded Flesh. She kills him.

The rescue shuttle arrives overhead and demands a safer landing site. The communication is cut before Cleaves can respond. Ganger Cleaves guesses the code word is 'Bad Boy' and calls the shuttle and orders it to the courtyard. Both versions of Cleaves are suffering simultaneous headaches. The Doctor says that she has a blood clot in her brain which is inoperable on Earth. She realises that he is not a weatherman after all. They leave the tower to go to the thermostat room in order to reset the cooling vents.

The other gangers find the second Doctor as he recovers consciousness and recruit him to their group.

The Doctor's party meets Rory. He tells them that Jennifer has found a secret tunnel not on the schematics through which they can escape, maybe back to the TARDIS. To get there they have to pass through the acid room. It is there that Rory and Jennifer's ganger lock the door. Rory is surprised at this, he just wants to tell the Doctor that the humans discard living ganger Flesh and that the world should know. Jennifer pulls him away back to the other gangers where he finds that she created a second ganger copy and killed the human Jennifer. A telephone rings and the Doctor takes a holographic phone call from Jimmy's son which he had set up earlier. The ganger Jimmy rushes off to release the human Jimmy but arrives just after the acid in the vat has boiled over, killing the human version. Jimmy's dying wish is that his ganger should replace him. Cleaves's ganger, too, is having a change of heart.

The Doctor and the survivors follow Jimmy's ganger back to the dining room. Jimmy finishes the phone call with Adam. The Doctor tells the boy that his daddy is coming home today

The Doctor tells everyone to run as the monastery begins to collapse. Jennifer, now a Flesh monster chases them. The Doctor gets them to a chamber and Dicken sacrifices himself closing the door against the monster. The Doctor and Cleaves's ganger barricade another door and the TARDIS drops in through the ceiling. Cleaves, Jimmy's and Dickens's gangers and Rory enter the TARDIS . Amy stops for the Doctor but he says that he is staying behind to keep the door shut. The shock for Amy comes when the two Doctors tell her that they swapped shoes, her only way of telling them apart, and the one she thought was the ganger was the real Doctor all along. She hugs the ganger and tells him he is twice the man she thought. He tells her to "push" and then says that he and the original Doctor had to find out the truth about Flesh, his purpose for going to the factory all along. The Doctor gives his sonic screwdriver to the ganger and then enters the TARDIS with Amy. As he goes he tells Cleaves's and the Doctor's gangers that they might still survive. The Doctor ganger uses the screwdriver to dissolve the monster outside, dissolving himself and Cleaves at the same time.

In the TARDIS the Doctor says that the energy of the time craft will permanently stabilise Jimmy and Dicken, making them into people. He also gives Cleaves a medicine that will cure the blood clot in her brain. He drops Jimmy off at a beach to be with his son and takes Cleaves and Dicken to an Army press conference where he tells them to spread the word about the gangers.

Back in the TARDIS, Amy is wracked with pain. The Doctor tells her she is in labour. The Doctor tells Rory to step away from her while he explains that their trip was so that he could get to see the Flesh in its early stages in order to learn how to stop the signal to Amy. He says that he and Rory will find her, wherever she is, then uses his sonic to dissolve her into a puddle of Flesh.

Amy wakes up in a white room. A panel opens in the wall to show the Eye Patch woman who tells her to push. Amy screams and the baby is on its way.