The Doctor and Nasreen explore the Silurian underground city, which appears to be deserted. The Doctor explains that most of the inhabitants are still in suspended animation, and they have to find Amy. They move toward the center of the city and the Doctor assures Nasreen that the front door is the best way to enter. They set off an alert and Silurian soldiers move in. The Doctor insists that they're unarmed and non-dangerous, In response, the Silurians gas him and Nasreen unconscious.
A Silurian scientist approaches Amy with a cutting blade, and then analyzes her clothing. He clamps Amy down and performs decontamination, and then begins dissection. However, he is interrupted by an incursion alert and a request for him to go there for species investigation. The scientist departs, unaware that Amy stole the remote for the controls. She frees herself and Mo and they slip out. As they go through the tunnels, Amy explains that they need to get to the surface and find the Doctor. She locates a cell and they find Elliot inside, tubes running into his body. Mo is unable to open the door and Amy assures him that his son is still alive. The worker agrees, but insists on finding weapons to rescue his son.
Ambrose is at the cemetery and Rory comes over. She realizes he's not the police as he claimed, and she demands to know why they are under attack. Rory insists that they need to keep their captive safe so they can exchange her for Mo and Elliot, and that they have to trust the Doctor.
The Silurian scientist, Malokheh, scans the Doctor while the head of the military, Restac, complains that they are wasting valuable time. Restac informs him that there's no word of Alaya, a member of her gene chain, and Malokheh begins decontamination process on the Doctor as the Time Lord screams in pain.
In the church cellar, Alaya is meditating when Tony comes in. She wonders why he isn't dead from the venom she injected into him, and he shows her his infected wound. Tony asks for a cure in return for an escape, and Alaya says she would rather watch the first ape death.
The Doctor explains that he's not an ape, and Malokheh confirms that he's not human. Restac objects but the scientist stops the decontamination process. The Doctor introduces himself and Malokheh explains that the drill was attacking their oxygen supply. Restac demands to know where the rest of their invasion force is, and the Doctor explains that they came to exchange Alaya for the human prisoners. Instead, Restac decides to send a message to the apes on the surface by executing the Doctor and Nasreen.
Amy and Mo find Silurians in suspended animation and open their cells. Amy notices that they're standing on a disc, while Mo notices tubes in the ceilings. She realizes that the discs are powered transports and they can use them to escape. Mo focuses on the weapons and vows to fight back. They get the weapons and seal the cells, and then continue on to a chamber filled with thousands of Silurian soldiers.
Tony is taking medicine when Ambrose finds him and realizes that something is wrong. She insists on inspecting the wound and assures him that he'll be fine.
As Restac and her troops take the Doctor and Nasreen away for execution, the Doctor explains that the Silurians went into hibernation when they detected an asteroid approaching the Earth. Instead, the Moon came into alignment with the Earth. Restac and Malokheh are surprised at the Doctor's knowledge, and he explains that he has met other tribes of Silurians in the past. However, he admits that the humans attacked them and they died. Restac vows anew to wipe out the apes.
Ambrose demands the cure from Alaya and promises to kill her if she doesn't get answers. Alaya dares her to kill her but informs Ambrose that she's too afraid. She thrusts herself at Ambrose, who tasers her, and then dares her to continue. Ambrose finally breaks and tasers her repeatedly. Rory is tending to Tony and hears Alaya's cries of pain, and runs to the cellar. He checks the Silurian while Tony tells his daughter that they have to be better than their enemy. Alaya tells Rory that she knew her death would come, and it will start the final war between Silurians and apes. She dies as Ambrose looks on in horror.
Malokheh objects to Restac's plans, but she ignores him and takes the Doctor and Nasreen to their court chamber. Amy arrives and holds the Silurians at gunpoint, but Restac easily disarms her when Amy is unable to shoot her in cold blood. She insists it's a military tribunal and sends Malokheh back to his laboratory. He has no choice but to go, but he warns that it isn't the way. They strap the humans and the Doctor to columns but then wait.
Tony holds her daughter, trying to reassure her, and they wonder what will happen. The power flickers and a TV monitor comes on, and Restac sends a transmission demanding to see the ape leader. Ambrose hastily covers up Alaya's corpse and Rory volunteers to speak. Restac confirms they have ape hostages and demands to see Alaya. Ambrose angrily refuses and demands her family back. The Silurian commander refuses and orders Amy's execution. The transmission cuts off, and Restac gives the order, but Malokheh arrives with their leader, Eldane. He orders her to release the prisoners and when she refuses, he invites her to shoot him. She backs down and demands to know why Malokheh favors the apes. He insists that they have evolved, and Eldane casually dismisses her. However, she warns that eventually they will need her.
The Doctor contacts Rory and assures him that everyone is fine. He has the Silurians send transport discs to bring Rory down with Alaya and then cuts off before Rory can tell him what happened to Alaya. Rory insists on returning her corpse to her people.
The Doctor talks with Eldane and Malokheh and suggests that Amy and Nasreen represent humanity in the negotiations. Amy wonders if the humans and Silurians resolve their difference in the future, piquing Nasreen's interest. After the Doctor explains that they travel in time, he informs Amy that the negotiations are a temporal tipping point that could create a new reality. Nasreen warns that no one will go for the idea of sharing the planet, but the Doctor insists, inspiring her. Amy and Nasreen sit down with Eldane and begin talking, while the Doctor takes Mo to get his son.
As Rory and the others prepare to go down, Ambrose takes Tony with her and says there's something they need to do. In private, Tony balks but she insists he needs to do it for his grandson.
Malokheh frees Elliot and explains that he's been studying the apes for the last three hundred years. He assures Mo he never meant to harm his child. The Doctor apologizes for losing track of him and Elliot accepts his apology. They go on and Malokheh tells them that he'll go on. However, the scientist then discovers that other cells have become operational and goes to investigate.
In the drill centre, Tony activates the systems.
Negotiations continue on and Nasreen warns that the planet can't sustain its current population, much less a new species. Amy suggests that the Silurians take the deserted areas of the planet, but Nasreen wonders what happen when the Silurians breed. Eldane offers new medicines and technology in return for the land. If they work together, the planet can achieve greatness. Nasreen agrees and the Doctor arrives to applaud their efforts. As they talk, the transports return.
Malokheh discovers that Restac has activated more of her soldiers. When he objects, she kills him.
Rory, Ambrose, and Tony arrive... carrying Alaya's body. The Doctor realizes that things have gone horribly wrong and Ambrose admits that she killed Alaya to save her son. Elliot backs away from her and the others stare in horror. The Doctor tries to reassure Eldane, but Ambrose insists that it is their planet. The Doctor condemns her and then looks up as Restac arrives with her soldiers. She looks down at her sister's body and mourns, and ignores the Doctor's pleas that it's only one woman. When the Doctor says the alliance could still work, Ambrose informs him that they've set the drill to begin again in 15 minutes. She offers to stop the drill if Restac and her people stay underground, but Restac orders their execution. The Silurians open fire and the Doctor uses his sonic screwdriver to blow out their weapons. He gets everyone to the laboratory while providing cover, claiming his sonic screwdriver is a deadly weapon. The Doctor tells them to go back into hibernation, but Restac insists on victory and the Doctor shorts out more of their weapons before retreating.
In the lab, Amy counts down the time until the drill begins. The Doctor realizes that Tony is ill and tells him that he's mutating rather than dying. He speculates that Malokheh's decontamination process could cure him. Restac and her soldiers surround the lab, and the Doctor suggests they send an energy pulse up at the drill to blow it up. Nasreen reluctantly agrees, but warns that it will cave in the surrounding tunnels. Eldane suggests they use the emergency fumigation system. The alarm will warn everyone to go into hibernation, and then shutdown the city. When the Doctor warns him he's betraying his people, Eldane admits that Earth isn't ready for him. The Doctor tells him to set the city to reactivate in a thousand years, and tells Elliot and the others to do what they can to prepare humanity for when their fellow planetary residents arrive. The Doctor negates the force field on surface and Eldane begins the decontamination process. However, he warns that the process hasn't begun on Tony. Tony tells them to go without him, and tells Elliot not to blame Ambrose for doing what she thought was right. Ambrose embraces her father and he tells her to go.
The fumigation process begins and Restac's soldiers retreat into hibernation, ignoring her orders. The Doctor opens the lab and sends everyone to the TARDIS, and apologizes to Eldane for the lost opportunity. Nasreen informs them that she's going to stay with Tony, her lover, and that they'll hibernate with the Silurians. When Tony is cured after emerging from hibernation, they'll have all the time they need. She thanks the Doctor and asks him to come look for them in a thousand years.
As the Silurians go back into hibernation and the city flood with fumigation gas, the Doctor and Amy get everyone to the TARDIS. However, as they enter, they see the time crack on the cave wall, and it's wider. The Doctor starts to investigate it, wondering why everyone knows about it except for him. He reaches into the crack and pulls out a piece of shrapnel. Restac arrives, dying from exposure to the hibernation gas. As she shoots at the Doctor, Rory shoves the Doctor away and takes the blast. As he lies dying, he remembers how their future selves were on the hill, waving to them. He apologizes to Amy and dies, Energy from the crack spreads toward Rory, and the Doctor warns Amy that if it touches her, she'll be wiped from history. Amy refuses to leave but she grabs him and pulls her into the TARDIS. Ignoring her pleas to go back, the Doctor dematerializes the TARDIS. Amy watches the light absorb Rory and insists the Doctor can't let her forget her Rory, but he leaves as Rory's body disappears. The Doctor tells her to remember Rory and tell him everything she knows about him to save his memory. She thinks about everything she knows about him, but the memories fade despite the Doctor's insistence. There's a shock to the TARDIS and the Doctor notices Rory's engagement ring, fallen from where Rory placed it earlier.
Everyone emerges from the TARDIS and they watch as the drill center explodes. They go back to the church and Ambrose wonders why the Doctor saved her from the Silurians. He insists that an eye for an eye is never the way, and now she has to show Elliot that there is another way, a way she couldn't be. As he returns to the TARDIS with Amy, they notice that now, only Amy is waving to them from the distant hill. The Doctor asks if she's okay, and she says she thought she saw someone else for a second. As they go into the TARDIS, the Doctor examines the piece of shrapnel he recovered from the crack: a part of the exterior TARDIS shell.