The Doctor/Ganger starts to suffer an overload of memories from past incarnations, and the Doctor tells his counterpart to hold on. The Ganger shoves him back and screams, his features going half-formed, and clutches at his head. Meanwhile, the Gangers cease their physical assault on the chapel doors and start burning through with acid. The Doctor/Ganger stabilizes and compares notes with its counterparts, and then the two of them step forward. Amy realizes that the real Doctor is wearing borrowed shoes since his were destroyed by acid. Both Doctors realize there must be a cable conduit
A minute later, the Gangers of Cleaves, Jimmy, and Dicken burn through the door and enter the chapel. Cleaves/Ganger realizes where the humans have gone and runs to the conduit just as the Doctor seals it and retreats with Cleaves.
Jennifer explores the catacombs and finds Flesh on the walls. As she explores, Rory watches her and follows.
As they move through the corridors and avoid the acid leaks, the Doctor asks Cleaves for a computer map of the maze of catacombs. The acid fumes react with the stone, causing a toxic gas and they head for the evac tower to get above the super-heavy fumes.
Cleaves/Ganger realizes that their enemy will head for the evac tower to avoid the gas, and it has a narrow door which her counterpart can easily defend. She clutches at her head as she suffers from another in a series of headaches.
As they get to the evac tower, Jimmy hears the bell toll midnight and realizes that it’s now his son’s fifth birthday. In the chapel, Jimmy/Ganger has the same realization and smiles. Jennifer/Ganger finds her comrades and tells them that she’s remembered that the eyes are the last thing to melt, and the last thing in them is a question: why? She wonders why they should suffer for the sake of human beings. Jennifer/Ganger suggests that they start a revolution of the millions of Gangers around the world. Cleaves/Ganger says that she just wants to live in peace, but Jennifer/Ganger warns that the humans will melt her and all of the others, and she remembers all the times that she was “executed.” The Jimmy and Dicken Gangers take her hands in a sign of support, and after a moment Cleaves/Ganger does as well. Jennifer/Ganger assures them that she has a plan that will destroy all the humans.
As the two Doctors work to restore power, they explain to Amy that the Flesh duplicated the Doctor after he scanned it. They notice that she feels more affection for the Doctor than his Ganger, and the Doctor/Ganger takes offense when she says he’s an almost-Doctor. The Doctor restores power and communication but Cleaves is unable to locate Rory or the Gangers on the internal scanners. She tries to call the mainland, but her Ganger anticipates her and intercepts the signal. Cleaves talks to a captain on the mainland, warns him of the situation, and demands that they wipe out the Gangers. She then types in a password for future verification, anticipating that her counterpart might be listening in. Cleaves/Ganger concedes that Jennifer/Ganger was right and they’ll have to fight to survive.
Jennifer/Ganger tries to access the Ganger-creation controls, but the security system locks her out as non-human.
As they prepare to evacuate, Buzzer warns that they can’t put themselves at risk to find Rory. The Doctor programs a transmission on delay, saying that he’s an optimist. As they talk, Amy notices a slot in the wall open so the Eye Patch Lady can look in. She realizes that no one else can see it, and the Lady disappears. The Doctor notices that she’s distressed and asks Amy what happened. She explains what she’s been seeing, but the Doctor dismisses it as a time memory, a mirage, and says that there’s nothing to worry about. The Doctor/Ganger says that there’s something in his head and walks out into the hallway. Amy goes after him and apologizes for her earlier comments, and asks if he can die. The Doctor/Ganger asks “why?” and then slams her into the wall. He explains that he can feel the Gangers each day, knowing that they will inevitably be “decommissioned” and all the Gangers can do is ask “Why?”
The Doctor/Ganger releases Amy, who runs into the evac chamber and tells the Doctor to keep his counterpart away from her. The Doctor has received the same telepathic impulse/question of “Why?”, but not as strongly. The Doctor/Ganger tries to apologize to Amy and then says that it can connect to the Flesh and realizes what it wants. When Cleaves admits that the Flesh cells can divide, the Doctor/Ganger warns that the Flesh wants revenge because it’s in pain. Amy and the others tell the Doctor/Ganger to remain where they can see it, ignoring the Doctor’s objections, and the Ganger reluctantly sits down.
Rory hears Jennifer calling out for help and goes to the Ganger generation chamber. He finds two Jennifers, each one insisting the other is a Ganger.
The shuttle arrives but is unable to land due to interference. The Doctor realizes that he can use the sonic screwdriver to differentiate humans from Gangers. Amy points out that means there is a difference between the Doctor and his Ganger, and the Doctor asks if she’s prejudiced.
Rory insists that he and the Doctor want both the humans and Gangers to live, but one Jennifer warns that the Flesh wants to kill them and there can be no cooperation. He notices that one of them is limping, and it shows the burn on her leg. The other Jennifer insists that it proves nothing and then attacks the first one, and her eyes turn white. The two Jennifers struggle and the real one knocks the Ganger into a puddle of acid, destroying it. The limping Jennifer tells Rory that they’re in it together and they go to find the others.
Buzzer detects Rory and Jennifer on the internal monitors, and Cleaves confirms that they’re heading for the thermostatic room. Amy suggests they go get them, and the Doctor tosses his sonic screwdriver to his counterpart. The others object, particularly Amy, but the Doctor insists. Buzzer reluctantly agrees to accompany it, and the Ganger assures Amy that they’ll find Rory. As they go, the Doctor tells Amy that he needs her to trust him and trust his Ganger counterpart.
Jennifer leads Rory to the thermostatic chamber and explains that they can recirculate the gas from there. She has him stand lookout while she goes inside, but then calls him inside and asks him to help turn a wheel. First Jennifer has him use his handprint to override the security lockout.
Cleaves realizes that Jennifer and Rory have shut down the underground cooling vents, allowing the stored acid to heat up and destroy the island. As Cleaves tries to reestablish contact with the shuttle, she clutches at her head in pain.
Dicken/Ganger notices that Cleaves/Ganger isn’t looking well, but she assures him that he’s fine.
Cleaves tells the Doctor let the issue of her headache go, but he confirms that it’s a peroneal clot. The monastery starts to break up, and Cleaves reestablished contact with the shuttle pilot. However, before she can give him the password, the comm system shorts out.
Cleaves/Ganger realizes that it’s their chance and tells the other two Gangers that she knows the password because “she” created it. She sends the pilot to the courtyard and gives the password, “badboy.” The pilot confirms and prepares to land, and she tells them that the Gangers will be incinerated.
Rory and Jennifer find a chamber filled with discarded half-melted Gangers. Jennifer explains that they are faulty but still conscious, trapped in hell. Shocked, Rory wonders how the company can do it and Jennifer asks who the real monsters are. He insists that they have to make people see the agony the Gangers go through, and Jennifer asks him to trust her.
The Doctor/Ganger and Buzzer try to find a clear human signal, and the Doctor/Ganger warns that the signal is fading. They find the real Jennifer just as she dies, and Buzzer asks who they saw with Rory. He then knocks out the Doctor/Ganger, saying it’s Cleaves’ orders.
As they head out, the Doctor and the others come to a wall with Flesh eyes attached to it. The Doctor says that the eyes were placed there to accuse them, and Cleaves says to ignore them.
Buzzer finds his way to the discard chamber and finds Jennifer/Ganger comforting the discarded Gangers. He accuses her of killing Jennifer, and Jennifer/Ganger says that she’s stronger now... and she can grow. Her mouth unhinges and she attacks Buzzer.
The Doctor and the others get to the thermostatic chamber and realize that they can’t stop the chain reaction. They’re forced to flee the chamber as the controls blow up, and find Rory in the corridors. He tells them that Jennifer has shown him a secret tunnel beneath the crypts. When Cleaves points out that there’s no such tunnel on the schematics, Rory says that it could lead to the TARDIS. They quickly head out, the Doctor last.
The Doctor/Ganger wakes up to find Cleaves/Ganger and the other two watching him. She warns him that the humans will always treat them that way, and that he’s one of them. In response, the Doctor/Ganger tells her to call him John Smith.
Rory leads the others into the Flesh chamber. Once they’re inside, Jennifer/Ganger shoves him aside and seals the door. When Amy wonders what he’s doing, Rory tells her about how the company has been discarding Gangers, and she and the others need to see. As the other Gangers arrive, the Doctor says that there’s no time and Rory asks Jennifer/Ganger if she’s sure about her plan. She tells him that the little girl she was got strong, and he realizes that the Jennifer he’s talking to is also a Ganger. Rory tries to open the door but Jennifer/Ganger yanks him away. Cleaves looks out at Cleaves/Ganger, who says that she’s sorry but they have to be free. The human says that she’s sorry too, because the Ganger has the same peroneal clots.
Back in the dining hall, Rory complains that Jennifer/Ganger created another Ganger to trick him, and the real Jennifer is dead. The Doctor/Ganger tells him that Jennifer is gone, and the pilot announces his final approach. When Rory goes to get the others out, the Doctor/Ganger stops him.
The Doctor has Dicken seal the acid vat in the hopes that it will stop the flood.
Rory tries to appeal to the Doctor/Ganger, who shoves him back and says “Ring ring” repeatedly. He tells Rory to stay put and the phone rings. The Doctor/Ganger answers it, and confirms that it’s a hologram call from Adam, Jimmy’s son. Jimmy/Ganger hesitates and the Doctor/Ganger says that he should talk to Adam, because the human Jimmy is dead. The Ganger runs off to save his human counterpart, and Jennifer/Ganger accuses the Doctor/Ganger of tricking him into an act of weakness. The Doctor/Ganger says that he’s shown him how to perform an act of humanity. Cleaves/Ganger tells Dicken-Ganger to drain the acid well, telling Jennifer/Ganger that there’s no point in a pointless war and that she’s become a monster... and Cleaves/Ganger doesn’t want her world populated by monsters. When Jennifer/Ganger says that she’ll get revenge on humanity, the Doctor/Ganger says that it doesn’t have to be about revenge but she ignores him and runs off.
Jimmy tries to keep the vat sealed, but acid spurts out and hits him in the chest. Jimmy/Ganger gets the door open too late and runs to his human counterpart’s side. The Doctor says that it’s too late, and the dying Jimmy tells his Ganger to raise Adam as his dad and gives him his wedding ring.
Adam asks for his father and as Jimmy/Ganger arrives with the others. He talks to “his” son and assures Adam that his father loves him very much. The Doctor and others then head for the courtyard, but find Jennifer/Ganger blocking their way. She transforms into a snarling multi-shifting creature and closes in. They run through one door and come to another, but realize that it can’t be locked. Dicken goes back to seal the first door and has to close it behind him. The others hear him scream for a second and then nothing.
As they close the other door, the Doctor/Ganger looks up and the TARDIS smashes through the ceiling. He tells everyone to get in, but Cleaves/Ganger and the Doctor hold the door shut as Jennifer/Ganger slams into it. Cleaves refuses to abandon her counterpart, but it tells her to go. Amy tells the Doctor that both him and his counterpart can survive. The Doctor/Ganger asks if he should sacrifice himself instead, and Amy says that he’s different. The Doctor at the door then explains that they swapped shoes earlier. She’s been talking to the real Doctor and assuming he’s the Flesh counterpart. They explain that they need to learn about the Flesh through her eyes. Amy hugs the Ganger, who tells her to push, but only when she tells her to. As Jennifer/Ganger starts to break through, Amy runs into the TARDIS with Rory. The Doctor tells his Ganger that with his molecular memory, he could survive, and then tosses him the sonic screwdriver. Cleaves/Ganger insists on staying with him as well rather than abandon her factory.
As the TARDIS dematerializes, the Doctor/Ganger explains that the sonic screwdriver can dissolve Jennifer/Ganger, but it will melt them as well. He says there may be a way out, and they’ll have to find out. They throw open the door and the Doctor activates the sonic screwdriver, and all three of them melt.
In the TARDIS, the Doctor explains that the artron energy will stabilize the Dicken and Jimmy Gangers, making them permanent beings. He finds a vial of medicine that will cure Cleaves’ clot and tells Amy that there are some happy endings. The Doctor takes Jimmy/Ganger to meet with his son, and then drops off Cleaves and Dicken/Ganger at the company headquarters. He tells Cleaves that she has to make the company understand what they’re doing to the Flesh, and make them stop. Cleaves goes in with Dicken/Ganger at her side. Once they’re gone, the Doctor once more tells Amy to breath. She asks why, but is then hit with stomach convulsions.
The Doctor and Rory get Amy into the TARDIS. He then explains that Amy is going into labor and having contractions. The Doctor tells them that he needed to see the Flesh in its early days and was going to drop them off, but they were caught up in the solar storm. He needed enough information to block the signal to the Flesh, and tells Amy that there was a signal to her. The Doctor then orders Rory to stand away as there’s something he needs to do. Rory hesitantly does so, and the Doctor tells Amy that they’re coming for her, no matter what it takes. When she says that she’s already there, the Doctor says she hasn’t been there for a long, long time. He aims his sonic screwdriver at Amy, triggers it, and she collapses into a pile of Flesh.
A pregnant Amy finds herself in a white chamber, laying on a platform. The Eye Patch Lady opens a slot in the wall and tells her that she’s ready to give birth. She tells Amy to push, and Amy screams in terror.