In the remote Welsh village of Cymtaff in the year 2020, Mo says goodbye to his dyslexic son Elliot and wife Ambrose and then rides off to the nearby mine. Tony Mack, Ambrose's father, and his coworker Nasreen Chaudhry watch as they hit a record in their quest to drill through the Earth's core. They leave for the night and Mo takes up his station. As he reads a book, the drill station starts to vibrate. The vibration fades but the security cameras go out one at a time. Mo goes to investigate as the lights flicker. He finds a smoking hole in the floor and reaches inside. It's filled with a layer of dirt and he reaches through... and something grabs his hand. He tries to pull free but a force below grabs him and pulls him down.
The TARDIS lands in the village cemetery, and the Doctor realizes that he's misnavigated yet again. He notices that the ground feels weird and thinks something strange is going on. Rory and Amy think he's trying to distract them, but the Doctor notices strange patches of blue grass around the cemetery. They notice two people on a nearby hill waving at them, and the Doctor uses binoculars to confirm that it's Amy and Rory's future selves, there to greet them. Amy wants to go see them, but the Doctor warns against it and takes an interest in the mining station. As he goes to investigate, Rory notices that Amy is wearing his engagement ring. He asks her not to wear it because it's so expensive, and takes it back to the TARDIS while Amy catches up to the Doctor.
Tony and Nasreen have found the hole, and wonder where it came from.
When Rory emerges from the TARDIS, he finds Elliot and Ambrose waiting for him. They think he's a crime scene investigator that they've called in, and take him to see the crime scene they reported.
The Doctor breaks open the gate to the mining station and goes inside with Amy.
Ambrose explains to Rory that her Uncle Alan died two weeks ago, and when they returned, they discovered that Alan had disappeared from his grave. There were no signs of digging from above, and apparently the body was removed through the bottom.
As they explore the mine tunnels, the Doctor still insists that something is wrong with the ground. They find Tony and Nasreen, and the Doctor identify themselves as government inspectors. The Doctor takes an interest in their readings and asks where the hole in the concrete floor came from. He says that they have to leave immediately, while steam starts to emerge from the hole. The station shakes and the Doctor uses the readings to confirm that the seismic shocks are confined to immediately beneath them. More holes open and the Doctor tells them to run. Tony steps through into another hole and Amy goes to help him. Another hole opens and Amy is pulled down. The Doctor grabs her, promising that he won't let go. As Nasreen pulls Tony to safety, the Doctor tells them to shut down the drill. He then tells Amy to keep calm and tries to pull her out. Despite his best efforts, she continues to sink and finally disappears from sight.
Rory investigates the bottom of the coffin without success. Elliot returns to ask him what kind of tea he wants, and suggests that the graves are hungry and eat people.
Tony wonders if the same thing happened to Mo, but the Doctor isn't sure. He realizes that something beneath the ground wanted Amy, and explains that whatever is responsible used bioprogramming to attack, something not present on Earth in this time period. The Doctor tells them to stay quiet, and then confirms they only have one drill. He notes that he hears drilling sounds coming from beneath the earth, modifies the sensors, and then asks why they drilled there. Nasreen explains that they found the blue grass, which contains minerals not seen in 20 million years. The Doctor explains that while they have been drilling down, something else has been drilling up. The sensors reveal heat signals that are moving toward the surface. The Doctor tells them to take the equipment and come with him, and explains that the sound they're hearing is a transport. Whoever bioprogrammed the earth is on their way up.
The Doctor leads Tony and Nasreen across the countryside and they notice strange glowing red energy in the sky. The Doctor fires a sling into it and realizes that it's a force field erected around the village. Rory arrives and tries to explain about the graves, and suggests they use the TARDIS. The Doctor warns they only have nine minutes until the transport arrives, and orders everyone into the church. Rory notices that Amy is missing, and the Doctor insists that he'll rescue her. Rory snaps at him, and the Doctor insists he needs him on his side.
Beneath the earth, a creature scans Amy's unconscious body.
At the church, Ambrose asks her father Tony what happened to Mo, but he doesn't have answers. She demands an explanation from the Doctor, and Elliot wonders if he can get Mo back. The Doctor says that he can, but asks them to do everything they say before it's too late. Ambrose hesitates and then asks him what he needs them to do. He tells them to set up a line of defense and place all of the recording equipment and motion sensors around the cemetery. They go to work and the Doctor finds Ambrose's Meals on Wheels van. Ambrose assembles weapons and the Doctor says that they don't need them, and asks her to put them away. Elliot draws a map of the area, and the Doctor explains that he'll send a sonic pulse through any sensor that detects the approaching intruders, stunning them. Elliot, impressed, asks if he's met monsters before and if he's scared of them. The Doctor says that monsters are scared of him, and he'll get Mo back. Elliot realizes that he's left his headphones at home and goes to get them. Meanwhile, the force field darkens, creating an artificial sunset, and the Doctor realizes that the intruders have arrived.
The Doctor, Ambrose, and Rory get back inside and they get a fix on the approaching intruders. The sensors burn out and the Doctor realizes that it's deliberate. The ground shakes and the Doctor realizes the intruders are directly below them. Ambrose realizes that Elliot is gone, and the Doctor admits that he saw the boy last. She blames him for letting her son go.
Elliot runs back through the cemetery, and humanoid creatures follow him. He gets to the church door and they try to get the jammed door open. The creatures close in and Elliot turns to face them. When the others get the door open, they discover that Elliot has been taken. Ambrose goes out into the cemetery and finds his headphones next to a hole in the earth, and cries in anguish. Another creature grabs her, and Tony attacks him. He shines his light on it, revealing a lizardlike humanoid. It stings him with an extendible tongue and runs off. The Doctor assures Ambrose that there's still hope and he'll find Elliot, but first he has to stop the attack and get everyone else inside.
The Doctor dons a pair of infrared sunglasses and walks into the village. He spots one of the creatures and realizes that it's cold-blooded. Returning to the church, he gets the fire extinguisher from Ambrose's van. When one of the creatures approaches him, he sprays it and Rory hauls it into the back of the van. The force field fades and the Doctor notes that both sides have hostages.
Amy wakes up and finds herself in a glass casket. She sees one of the creatures outside and demands that it release her. Instead it pumps gas into the casket, rendering her unconscious.
The Doctor explains to Rory that he thinks that he knows what the creatures are, and that he's met a different branch of them before. He goes to the church cellar where they've confined their prisoner in chains. The Doctor introduces himself and removes its mask. Beneath is a female creature and the Doctor says that she's beautiful. He then identifies her as a remnant of a bygone Earth age and admires her form of transport. The Doctor then asks her to return Amy, and wonders why they have returned to the surface. The creature says that she's the last of her species, but the Doctor doesn't believe her and says he knows how it really feels to be the last of ones species. The creature identifies herself as Alaya and the Doctor asks what woke up her people. She says that they were attacked by the drill, and their life support systems activated the warrior class to deal with the assault. Alaya views humans as vermin, but the Doctor offers to broker a peace. He warns that they are seriously outnumbered, and asks for the return of the three abductees. Alaya refuses and the Doctor insists that he won't let her provoke a war. She warns that a massacre is due, and is willing to die for her cause.
In the church, the Doctor explains that he's going to go below to find Amy and the others, and the creatures they're dealing with are known as Silurians, homo reptilian
. He notes that the drill was threatening the Silurians' settlement, and he needs Alaya alive as a bargaining chip. The Doctor tells them to act as the best of humanity, but Tony wants to dissect the creature to find out their opponents' weaknesses. The Doctor insists they have to represent humanity in its best possible light, and he won't let anyone die today. Nasreen applauds but Ambrose and Tony aren't nearly as impressed.
The Doctor goes to the TARDIS and Nasreen wants to go with him. He says she should stay behind and Tony agrees, but Nasreen insists and the Doctor gives in. She's duly impressed at the spacious interior, but the TARDIS is caught in a magnetic field and pulled beneath the earth.
Rory, Tony, and Ambrose go to see Alaya. The Silurian warns that eventually one of them will kill her, setting off the war she wants that will lead to the extermination of the ape vermin. Afterward, Tony goes off in private and examines the wound on his neck. Lines of green are spreading throughout his body.
The TARDIS comes to a halt and the Doctor opens the exterior doors. They are in an underground tunnel more than 20 kilometers beneath the Earth, and go exploring.
Amy finds herself strapped into an examination table next to Mo. He explains that she will undergo contamination and then be vivisected, just like he was. A Silurian male enters with a medical cutting tool and advances on Amy.
As they explore, the Doctor figures that they're looking for a small tribe of Silurians. However, they find a vast chamber filled with thousands of Silurians, and the Doctor realizes that he's miscalculated.