It is 2020, in the Welsh village of Cwmtaff. A drilling team led by Dr. Nasreen Chaudhry reaches a depth of twenty one kilometres. They are attempting to drill deeper than anyone before, trying to investigate minerals that have appeared in the district but have not been found on the surface of the planet for over 20 million years.

The mining team clock off for the night, leaving Mo Northover, a night watchman, in control. He notices a trembling and the lights and cameras start to fail. He goes to investigate and finds a steaming hole in the ground. He reaches into a sudden covering of soil and is dragged beneath the surface.

The Doctor arrives with Amy and Rory. He has told them that they are going to Rio de Janeiro but overshot. He is intrigued that the ground feels wrong and there are patches of blue grass in the graveyard where the TARDIS has landed. The trio notice a couple waving to them from the distance. The Doctor looks at them through his binoculars and realises that it must be future Amy and future Rory. His attention is distracted by a 'big mining thing' and he decides to go and have a look.

Rory takes Amy's engagement ring back into the TARDIS for safekeeping and, when he exits, he finds that the other two have gone on without him. Instead he meets Ambrose Northover and her son Elliot. She thinks that he is a policeman responding to her call. She tells him that a family grave has been dug up and the coffin removed without disturbing the ground. Rory decides to investigate.

The Doctor and Amy break into the plant just after Dr. Chaudhry and her assistant, Tony Mack, have arrived to find Mo missing and an unexplained hole in the floor. The Doctor introduces himself as a ministry official and declares that their readings are wrong: the ground beneath them is moving without explanation. The room trembles, more steaming holes appear and the Doctor tells the others to run. Mack is trapped in a hole but Amy pulls him free only to get stuck herself. The Doctor tells them to shut the drill down but by the time they do Amy has gone. The Doctor surmises that the ground has been bio-programmed to attack whenever it perceives a threat. Even though the drill has stopped the Doctor hears more drilling. He hacks into the company records and tells the others that while they have been drilling down, somebody else has been drilling up. On a monitor, he shows them that three objects are heading for the surface. He calculates that they will arrive in twelve minutes.

The Doctor, Dr. Chaudhry, and Mack head out of the compound and meet up with Rory, Ambrose, and Elliot. A dome shaped energy barrier appears around the village. Rory asks where Amy is but the Doctor can only promise to get her back. Ambrose learns that her husband is missing, too. The Doctor promises to get him back, too, but asks that they all trust him. He asks everyone to get every phone, camera and piece of transmitting equipment they can find. While the adults set up a network of cameras, he asks Elliott to draw a map of all of the cameras.

Elliot shows the Doctor his map which draws an appreciative comment. The Doctor says that being dyslexic shouldn't hold anyone back. In a brief exchange, the Doctor talks about how he misses his home, how monsters are scared of him and how he will get Elliot's dad back. Next, the Doctor sees Ambrose collecting weapons and asks her to put them away. The dome goes dark to cut out their light and the adults retreat into the church but Elliot has gone home to collect his headphones from his house. An energy surge into the church wrecks the systems.

Elliott is chased back to the church and captured before the people inside can get the door open to save him. Ambrose and Tony run out into the graveyard and Tony is lashed with a venomous tongue by a reptilian humanoid. The Doctor and Rory are capture one of the reptiles by bundling it into the refrigerated Meals-on-Wheels van that Ambrose drives. The Doctor remarks that the enemy are leaving but both sides now have hostages. Daylight returns.

Amy awakes in what she presumes to be a glass coffin. She shouts for help but is shushed by someone looking in. Gas fills her chamber and she passes out.

The Doctor takes his prisoner, Alaya, a warrior of a Silurian tribe, taken into the church where he talks with her. He tries to broker a peace with her but she insists that the humans have attacked her people with their drill and the warrior class has been awoken to defend their tribe. She says that the Silurians will wipe humanity off the surface of the planet.

Tony wants to dissect Alaya to find the Silurians' weak points. The Doctor argues that the Silurians feel they have as much right to the planet as the humans and that they are not evil. He says he is going underground to find their friends and family but he want s the others to remain behind and be the best that humanity has to offer.

The Doctor, accompanied by Dr. Chaudhry, enters the TARDIS to meet the Silurians underground encampment. While the TARDIS is suddenly pulled down into the earth, the others visit Alaya. She says that one of them is going to kill her and she knows who.

Amy awakens in a dissecting chair. Beside her is Mo, with a huge scar running down his chest. A Silurian surgeon closes in on her.

The Doctor and Chaudhry exit the TARDIS. He tells her they may find a small settlement and a dozen Silurians. Instead they find a vast, underground city.

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.