The Doctor and Nasreen enter the city, using what the Doctor calls 'front door approach'. Silurian troops capture them immediately.
Malohkeh, the Silurian doctor, is about to start dissecting Amy, but is called away to examine the Doctor. Amy releases herself and Mo after picking the surgeon's pocket. They find Elliot in suspended animation. He is wired up to machines but Amy says that they will get him out.
Rory promises Ambrose that they will get her family back and that he trusts the Doctor.
The Doctor and Nasreen are strapped to machinery in a laboratory and the surgeon starts to decontaminate the Doctor, causing severe pain. Malohkeh stops the procedure, against the wishes of Commander Restac, when the Doctor says that the procedure will kill him. He asks for celery.
Tony asks Alaya to cure him of the venomous sting on his shoulder in exchange for her release. Instead, she taunts him, saying that he will be the first ape casualty of the coming war. Restac says she will have the Doctor executed as a clear message to the surface. He tries to offer them a prisoner exchange but the drill's proximity to the oxygen pockets above the city are interpreted as an act of war.
Amy and Mo move through the corridors until they find two Silurians in suspended animation. They deduce that the reptiles are standing on discs that will lead up through tubes to the surface. They relieve the two soldiers of their weapons and move on but enter a vast chamber with an army of warriors standing ready. Amy says that they need to find the Doctor.
The Doctor and Chaudhry are led through the city. He explains to her that the Silurians put themselves into suspended animation when they thought that another planet was going to collide with the Earth. In fact, it was the moon coming into alignment with the Earth. Restac overhears and asks how he knows this. He tells her he met others of her species, similar but different. He adds, under questioning, that the humans killed them.
When Ambrose sees how severely hurt her father is she uses a Taser on Alaya to try to get a cure from her. Alaya continues to taunt her, goading her into using the Taser again until it kills her. Tony and Rory find the dying Silurian and Tony tells his daughter that they have to be better than this.
The Doctor and Chaudhry are taken into the Silurian court, also their place of execution. Amy and Mo enter but are unable to bring themselves to use their weapons and are overpowered. The prisoners are chained to pillars. Malohkeh tells Restac that this is not the way to behave but she says that it is war and the executions will begin.
Restac calls the humans in the church and asks to see Alaya. Ambrose refuses and Restac orders the execution of Amy. The screen Restac has been talking through goes blank. Before the Silurians can open fire, the Silurians' leader, Eldane, is brought into the court by Malohkeh and tells them to stop. He says that the humans have evolved and that war is not the way forward. The Doctor is able to call back to the surface and tells the others to come down, bringing Alaya with them.
The Doctor sets up a conference between the Silurians and humans with Amy and Nasreen as ambassadors for humanity. He tells them that there are fluid points in time and that this is their chance to create a timeline that will shape the future of the planet. Malohkeh releases Elliot to his father, saying that he never harms the young. As the Doctor and the two humans return to the chamber, Malohkeh is killed by Restac.
Amy, Nasreen and Eldane discuss how the Silurians might live alongside humans. The Doctor enters and is pleased with their progress. However, Rory enters with Ambrose and, behind them, Tony Mack carrying the body of Alaya. Ambrose confesses and her family stare at her, aghast. The Doctor berates her for being so much less than the best of her species. Restac and her warriors enter. When she sees the corpse of her sister she begins to cry and then orders her warriors to open fire. Ambrose tells them that she had her father set the drill to resume its downward course in fifteen minutes. The Doctor uses his screwdriver to disarm the warriors, causing their guns to explode in their hands, while the others flee to a control room.
Eldane tells them that he will release toxic gas, originally designed to defend the city. It means that Silurians in suspended animation will be safe, but the others will be killed. The Doctor asks Chaudhry to use an energy surge to destroy her drill and, as she points out, her life's work. The Doctor asks Mo and Ambrose to begin spreading the word that the Silurians will return in one thousand years and that it will be time then to share the planet.
Tony decides to stay so that the Silurians can cure genetic mutation brought on by the sting in his shoulder. Chaudhry says she will stay too. Having found what she was looking for she does not want to leave it so soon. The Doctor tells everyone to run to the TARDIS where he opens the door and orders them in.
He sees a crack in the wall beside the TARDIS. Amy recognises it as the one from her bedroom wall. The Doctor remembers Prisoner Zero and the Angels taunting him because he didn't know what it was. He goes to the crack to find shrapnel and pulls out a piece of debris. As they go to the TARDIS, Restac arrives, and shoots at the Doctor, but Rory pushes him out of the way and is shot instead. The Doctor makes Amy leave him before Rory is swallowed by the crack, thus erasing him from history. The only thing that remains of Rory is the engagement ring.
The TARDIS lands as the drill is destroyed by the Silurian energy surge. Amy sees herself again, on the hill, this time alone. As she re-enters the TARDIS, the Doctor looks at what he pulled out of the crack: a scorched piece of the notice from the TARDIS door.