The Doctor confronts his Ganger counterpart, who begins suffering from regeneration crisis. After a few minutes, the Doctor-ganger manages to stabilize. Meanwhile, the attacking Gangers briefly stop their assault on the chapel door, but then get acid and start burning through the metal. The Doctor and his Ganger compare notes, are duly impressed with each other's superior intelligence, and then step forward to address Amy, Cleaves, Dicken, Buzzer, and Jimmy. Amy notices that "her" Doctor is wearing the borrowed shoes, while the Doctor-Ganger is wearing the duplicated shoes he was wearing before they were destroyed by acid. Both Doctors deduce that there must be a large cable conduit entering the chapel.
The Ganger Cleaves, Jimmy, and Dicken burn through the door and enter the chapel. Cleaves-Ganger, with her human counterpart's knowledge, realizes where their intended victims have gone, and goes to the conduit just in time to see the Doctor seal the access hatch and retreat with Cleaves and the others.
Jennifer explores the stone corridors and finds globs of Flesh stuck to the walls. As she continues on, Rory cautiously follows her, unsure if it's Jennifer or her Ganger counterpart.
The Doctor realizes that the need a computer map of the monastery to make their way through the catacombs. They come to a chamber filled with rising levels of a white gas, and the Doctor realizes that the acid from the leaks is reacting with the stone, releasing an asphyxiation gas. Since the gas is heavier than air, they head for the evac tower to get above the toxic fumes.
Cleaves-Ganger notices the gas and realizes that their enemy will head for the evac tower. When the other two Gangers suggest they attack, the Ganger warns that it has a single easily-defensible door. Before she can come up with a plan, Cleaves-Ganger clutches at her head and complains about a headache.
In the evac tower, Jimmy hears the monastery bell toll midnight and realizes that it's his son Adam's fifth birthday. His counterpart in the chapel remembers the same thing, having all of his counterpart's memories.
Jennifer-Ganger enters the chapel and tells them that the eyes are the last things that melt, and they always have the same question: why? She insists that they shouldn't be forced to suffer for the sake of humans, and proposes a revolution. Jennifer-Ganger wants to lead the millions of Gangers worldwide in rebellion, but Cleaves-Ganger just wants to live in peace. However, Jennifer-Ganger warns her that the humans will decommission all of them rather than risk an uprising. She is keen on revolution because, unlike the other three Gangers, the solar storm that brought them all to life also let her feel the memories of the dozens of time she had been "executed" in the past. The Dicken and Jimmy Gangers take her hand and lend their support, and they look to Cleaves-Ganger. After a moment's hesitation, she does as well, and Jennifer-Ganger tells them that she has a plan to wipe out the humans once and for all.
In the evac tower, the two Doctors try to restore the power and explain that the Flesh scanned the Doctor earlier and made a duplicate of him. It soon becomes clear that Amy distrusts the Doctor-Ganger, dismissing him as an "almost-Doctor." The Doctor restores power but they are unable to locate Rory or Jennifer on the internal scanners. She calls the mainland, while in the control chamber her counterpart anticipates her move and taps into the transmission. Cleaves calls her superiors on the mainland and asks for evacuation, and recommends that they destroy the Gangers. Anticipating a ploy by her counterpart, Cleaves then types in a password so that anyone listening in can't identify it, and tells the evac captain to only take her orders if he receives the password. Cleaves-Ganger and the others realize that they are in a fight for their survival.
Jennifer-Ganger goes to the thermostatic chamber and tries to access the controls, but the security system identifies her as non-human and locks her out of the system.
Amy insists on finding Rory, but Buzzer refuses to put themselves at risk. The Doctor programs in a telephone call but refuses to say who it is for. Instead he merely says that he's an optimist. As they prepare to evacuate, Amy looks up and sees a slot in the wall open and the Eye Patch Lady appear. When she glances at the Doctor, she realizes that he can't see it. The Lady closes the slot, which disappears, and the Doctor asks Amy what she saw. When she describes the Lady, the Doctor says that it's a time mirage brought on by vortex travel and tells her not to worry about it. The Doctor-Ganger clutches at his head in pain and then runs out into the corridor. Amy goes after him and asks if he's okay, and then apologizes for her earlier dismissal of him. He grabs her and slams her into the wall, and says that he can feel the deaths of the Gangers each day, and that they can remember the constant pain but can only ask "Why"? He finally releases Amy, who runs back into the evac chamber and tells the Doctor to keep his counterpart away from him. The Doctor says that he is picking up a much weaker telepathic signal of the Gangers' pain, while the Doctor-Ganger says that he is linked to the Flesh and knows what it wants: revenge for the pain the humans have inflicted on it by killing the Gangers over and over. Despite the Doctor's objections, the others consider the Doctor-Ganger a threat and tell him to sit down on a barrel where they can keep an eye on him.
Rory hears Jennifer calling for help and goes to investigate. He finds her in the Ganger creation chamber, limping... and another Jennifer is also present. Each accuses the other of being the Ganger.
The evac shuttle arrives but is unable to land due to interference from the solar storm. The Doctor sonics his counterpart and then Cleaves, and informs them that he can use the sonic screwdriver to tell human and Gangers apart. When Amy says that means there is a noticeable difference, the Doctor asks if she's prejudiced.
Rory tells both Jennifers that he and the Doctor want to have the two sides reconcile, but one Jennifer insists that the Flesh wants all humans dead. He points out that the first Jennifer is limping, and it shows him that she has an acid burn on her leg. The other Jennifer insists that the burn proves nothing, but then her eyes turn white and she attacks the first Jennifer. The two of them struggle, ignoring Rory's attempts to stop them, and the limping Jennifer finally pushes the other one into a pool of acid. It dissolves into Flesh and "dies," and the real Jennifer tells Rory that they have to find the others.
Buzzer finally locates Rory and Jennifer on the internal monitors, and confirms that they're heading for the thermostatic chamber. Amy insists on going after them, and the Doctor gives his sonic screwdriver to his Ganger counterpart as a gesture of trust. The Doctor-Ganger offers to help find Rory, and Buzzer accepts his help. As they go, the Doctor tells Amy that she has to trust both of him.
Jennifer takes Rory to the thermostatic chamber and asks for his help recirculating the asphyxiation gas. She calls him inside and asks him to use his handprint to unlock the security system so she can vent the gas. Rory does so and the security system confirms that he's human and grants them access.
Cleaves confirms that Jennifer has shut down the acid cooling vents. The stored acid begins to heat up, and Cleaves warns that the resulting explosion will soon destroy the entire island. Cleaves tries to contact the evac shuttle and winces in pain from a headache.
Dicken-Ganger notices that Cleaves-Ganger still has her headache, but she insists that she's fine.
The Doctor notices Cleaves' headache and diagnoses that she has an inoperable clot. The monastery starts to collapse, and Cleaves contacts the shuttle pilot. She starts to give him the password but the comm system shorts out. In the control chamber, Cleaves-Ganger seizes the opportunity and tells her comrades that she knows the password because her human counterpart used the same one that she would have. Breaking in on the signal, Cleaves-Ganger sends the shuttle pilot the password, "badboy," and he confirms that it's correct. She tells him to land in the courtyard instead. When he asks about the Gangers, she tells him that they will be incinerated with the island blows up.
Jennifer leads Rory to a chamber filled with dozens of discarded, half-melted Gangers of herself and the others. One of them opens its eyes and Jennifer explains that they were discarded as faulty, but are still conscious and can feel everything that has been inflicted on them. Shocked, Rory wonders how the company and do that, and Jennifer asks him who the real monsters are. He wants to let everyone know the pain that the Gangers feel, and Jennifer says that there's a way but she needs him to trust her.
The Doctor-Ganger uses the sonic screwdriver to track Jennifer's life signs, but warns Buzzer that they're fading. They find her just as she dies, and Buzzer wonders who they saw with Rory on the monitors earlier. H knocks out the Doctor-Ganger and tells him that he's acting on Cleaves' orders.
The others head for the rendezvous with the shuttle and find a wall covered with Flesh blobs. They have grown eyes, and the Doctor says that they were placed there to accuse them. Cleaves says to ignore them and they continue.
Buzzer hears Jennifer and goes to the chamber with the discarded Gangers. He realizes that "Jennifer" is actually her counterpart when he sees her soothing the discards. Jennifer-Ganger admits that she killed Jennifer, and that now she can grow. Her mouth unhinges and she lunges at Buzzer.
When the Doctor's party arrives at the thermostatic chamber, they realize that a chain reaction has started and there is no way they can stop the explosion. The controls blow up and they flee outside, and find Rory waiting for them. He tells them that Jennifer has shown him a secret tunnel out of the monastery, even though Cleaves says that there isn't one on the schematics. Rory assures them that it leads beneath the TARDIS and they follow him.
Cleaves-Ganger and the other two find the Doctor-Ganger as he wakes up. She points out that the humans will never trust them, and that he has to aid them because he's one of them. The Doctor considers and then tells her to call him John Smith, not the Doctor.
Rory leads the others into an acid chamber. However, once they're inside, he retreats and Jennifer-Ganger seals the door. Amy goes to the portal window and asks Rory what he's doing, and he explains that he and Jennifer-Ganger have locked them in to make them see what the discarded Gangers go through. However, the other Gangers arrive and Rory wonders what is happening. Jennifer-Ganger says that she's not the weak little girl she was as a human child, and Rory realizes that she's the Jennifer-Ganger that he talked to earlier, the one that was seemingly destroyed. Realizing that he's been tricked, Rory tries to free Amy and the others but Jennifer-Ganger stops him. Cleaves goes to the window and looks accusingly at her counterpart, who insists that they have to do whatever it takes to be free. Smiling knowingly, Cleaves says that she knows her Ganger has the same clot and she picked the wrong human to be based upon.
The Gangers take Rory to the dining hall, and he accuses Jennifer-Ganger of tricking him by creating a second version of herself. He blames her for killing the human Jennifer, and the Doctor-Ganger tells him that Jennifer is gone. As the evac shuttles comes in for its final approach, Rory tries to go free the others but the Doctor-Ganger stops him.
The Doctor tells Dicken to seal the vat with the overheating acid in the hopes it will contain it, but admits that the odds aren't good.
The Doctor-Ganger ignores Rory's appeals for help and yells "Ring ring!" A hologram call from the mainland comes in and the Doctor-Ganger answers it. It's Adam, Jimmy's son. Jimmy-Ganger hesitates but the Doctor-Ganger says that the human Jimmy is dead by now and the Ganger is the only father that Adam has. Confronted with the knowledge that he and the others are committing murder, Jimmy-Ganger runs off to save his human counterpart. Jennifer-Ganger accuses the Doctor of tricking Jimmy-Ganger into an act of weakness, but the Doctor-Ganger insists that it's an act of humanity. Cleaves-Ganger takes command tells Dicken-Ganger to drain off the acid in the chamber. She tells Jennifer-Ganger that the latter was once an innocent girl, but now she's become a monster and Cleaves-Ganger doesn't want a world populated with monsters. Jennifer-Ganger insists on getting revenge against humanity and runs off.
Jimmy tries to hold down the lid of the vat, but acid spurts out, hitting him in the chest above the heart. Jimmy-Ganger arrives too late and goes to his human counterpart. As he dies, Jimmy tells the Ganger to raise Adam as his own son and gives him his wedding ring.
Back in the dining room, Adam asks to see his father. The Jimmy-Ganger returns and assures Adam that everything is fine and his father loves him very much. The Doctor and the others head for the courtyard, but Jennifer-Ganger blocks their way. As they watch, she transforms into a mutated creature with extended limbs. She comes after them and they retreat through one door and then to another. The second door doesn't lock, and Dicken goes back to the first door. With the Jennifer monster closing in, Dicken closes the first door, sacrificing himself as the others hear his screams of agony.
The others manage to close the second door, and the Doctor-Ganger looks up at a spot in the corridor. The TARDIS crashes down through the ceiling, and the Doctor-Ganger tells everyone to get in. The Doctor and Cleaves-Ganger refuse, saying they have to hold the door shut as the Jennifer monster slams into it, trying to break through. Cleaves refuses to go, but her counterpart tells her to escape while she can.
Amy tells both Doctors that they can escape, but the Doctor-Ganger asks if he should sacrifice himself. She admits that if one of them has to, she would rather that he do so because he's the different one. The Doctor at the door steps forward and then explains that he and his counterpart swapped shoes: the Doctor that Amy has considered the real one is actually the Ganger. They performed the ruse to learn about the Flesh through her eyes. Amy hugs the Doctor-Ganger, who enigmatically tells her to push, but only when "she" says to. Amy enters the TARDIS with Rory, Cleaves, Jimmy-Ganger, and Dicken-Ganger, and the Doctor tells his Ganger that he may be able to survive. He then tosses the Doctor-Ganger the sonic screwdriver. The Doctor-Ganger tells Cleaves-Ganger to go, but she refuses to abandon her factory.
The Doctor enters the TARDIS and departs, and the Doctor-Ganger explains to Cleaves-Ganger that he can set the sonic screwdriver to dissolve all Flesh in the vicinity. However, it will destroy the two of them as well, although there may be a way out. When she wonders what it is, the Doctor-Ganger says they'll just have to find out. He opens the door and activates the sonic screwdriver, and all three of them dissolve.
In the TARDIS, the Doctor tells the Jimmy and Dicken Gangers that the energies of the vessel will make them permanent. He finds a vial of medicine that cures Cleaves' clot, and tells Amy that there are some happy endings. The Doctor then pilots the TARDIS to a beach where Jimmy-Ganger is reunited with Adam for the first time, and then goes to the company lobby. He tells Cleaves and Dicken-Ganger that they have to make the company understand what is being done to the Gangers and stop them. They go in together to meet the press.
As they watch, the Doctor tells Amy to breath. She clutches at her stomach in pain, and the Doctor and Rory usher her into the TARDIS. As they depart, the Doctor explains that Amy is going into labor and the stomach pains are contractions. He informs his companions that he went to the monastery to see the Flesh in its early days. The Doctor had planned to keep them out of it, but they were swept up in the solar storm before he could drop them off for fish and chips. When they wonder why, the Doctor explains that he needed enough information so that he could block off a signal... a signal to Amy. He orders Rory to stand away from Amy. Realizing what has happened, Rory slowly backs away. The Doctor then addresses Amy, saying that they'll come for her and rescue her no matter what it takes. When she says that she's already there, the Doctor says that she isn't, and hasn't been for a long time. He activates his sonic screwdriver and she melts into a blob of Flesh.
Amy wakes up on an operating table in a white chamber. The Eye Patch Lady opens a slot in the wall and tells Amy that it's time for her to give birth. She tells her to push and Amy screams in terror and pain.