Egypt, 1334 BC
The Doctor tries to return to the TARDIS but Queen Nefertiti doesn't want to let him leave after what they shared defeating a giant alien locust attack. He detects a temporal reading and finds it exciting, and Nefertiti grabs him and throws him into the TARDIS.
Earth, 2367 AD
The Doctor and Nefertiti arrive and Indira with the India Space Agency informs him that an enormous space ship is heading for Earth. They have readings from their drones and the Doctor is intrigued by what they show. ISA has received no response to their hails and they plan to blow it up if it comes within 10,000 kilometers of Earth. The ship will get that close in just over six hours and the Doctor goes to get help.
African Plains, 1902 AD
The Doctor meets with big-game hunter John Riddell, who has been waiting for him since he popped out for licorice seven months ago. He's immediately intrigued by the Doctor's suggestion that there is something intriguing to investigate.
London, Present Day
At the Pond home, Rory's father Brian stops by to fix the lights. As he puts down Rory, the TARDIS materializes around them and he assures them he has something interesting to show them. They materialize inside the approaching spaceship and step outside, and Amy and Rory try to explain what's going on to Brian. When the Doctor finally notices Brian and asks if he's a stowaway, Rory explains who he is and the Doctor performs introductions. As Rory starts to explain, something starts shaking the ship and Amy complains that it's been ten months since they last saw the Doctor. A door opens and two ankylosauri charge out.
The group finally takes refuge in a room off the corridor. Riddell offers to kill one of them but the Doctor insists that they have to preserve them. Once the dinosaurs continue on their way, the Doctor tries to figure out what's going on and Brian takes it all in. They're unaware that they have triggered an intruder alarm. The Doctor finds a computer control panel and confirms that different sections of the ship have different engines. He finds the primary cluster and asks the computer for directions, and the Doctor, Rory, and Brian are teleported away. They find themselves on a beach and Brian demands to know where they are. The Doctor tells them that it doesn't taste like Earth and Rory points out that the beach is humming. While Rory and Brian dig, the Doctor goes looking at rocks. Brian produces a trowel and confirms that there's a metal layer just below the sand.
On the ship, the captain listens to the three men and takes an interest when Rory refers to "The Doctor." He tells his robots to bring them to him.
Amy, Nefertiti, and Riddell continue exploring and realize there are more dinosaurs aboard the ship. Nefertiti introduces herself, impressing Amy, while they discover that they're standing over a sleeping baby Tyrannosaurus Rex. Once they move clear, Riddell introduces himself and Amy admits that she's never heard of him.
The Doctor finds a hidden computer panel and confirms that they're still on the ship in the engine room, and it looks like a beach because it uses hydrogenerators. He can't shut the engines down in time and then points out that there are pterodactyls flying toward them. They run for it as the Doctor explains that the teleporter out when they arrived. The trio gets into a cave just in time but something large approaches them from inside: two battle robots, who announce that they're very cross with them.
Amy, Riddell, and Nefertiti find another abandoned section of the ship and speculate that something wiped out the crew. When Amy fiddles with the controls, she brings up the data records while Riddell catches a glimpse of a dinosaur behind them. They finally access a video of the ship's commander, a Silurian named Bleytal, who explains that they evacuated Earth to avoid the oncoming collision with the moon.
The robots take the Doctor, Rory, and Brian back into the ship and the Doctor and Rory go along, figuring the robots will take them to their leader. A triceratops comes up and smells the grassy residue on the golf balls that Brian has in his pockets. The Doctor has Brian toss one away and the triceratops goes after it.
Bleytal explains that of the fifty species they've loaded onboard, all but one is adopting and the Silurians expect them to reproduce and repopulate once they return to Earth. While Nefertiti and Riddell argue and flirt, Amy brings up the lifesigns for Silurians on the ship but discover that there are none onboard. Amy compares the historical records with the current lifesign readings and discovers that there is another spacecraft at the center of the Silurian ark.
The robots take the Doctor, Rory, and Brian to the intruding spacecraft and open the gate for just the Doctor. He continues on and the captain, Solomon, greets him from his life-support couch. Solomon apparently knows the Doctor, claiming that it's Fate that he came. A beam briefly shines on the Doctor and Solomon claims that it's a system malfunction. He explains that three raptors attacked him and the robots rescued him just before it was too late. Solomon wants the Doctor to help him, assuming he's a medical doctor, and the Doctor examines him. He offers to help if Solomon explains about the dinosaurs, and Solomon orders the robots to injure Brian. One of them wounds the elder Williams and Solomon warns that he doesn't like questions.
Rory tends to his father's injury, applying a burn pack. Brian thanks him, much to Rory's surprise. Rory's phone rings and he takes it. It's Amy and they compare notes. Meanwhile, Solomon asks the Doctor how he came onboard but the Doctor avoids the question and asks how Solomon's ship became embedded in the ark. Solomon explains that he's transporting it to a colony to sell the dinosaurs. The beam that scanned him is connected to a database system that can calculate the value of anything. However, Solomon is surprised to discover that the Doctor isn't in his database. As the Doctor completes his work on Solomon's legs, Rory gives him the phone and Amy tells him about the missing Silurians. As he gives the phone back to Rory, he tells his companion to be ready.
Solomon thanks the Doctor for his help and he asks what happened to the Silurians. The trader admits that the robots jettisoned them from cryosleep and ejected them into space so he could claim the extinct dinosaurs when the Silurians refused to negotiate. The Doctor, thoroughly disgusted, wonders why he's off-course and heading for Earth and then realizes that Solomon doesn't know how to turn off the pre-programmed coordinates. Solomon orders the Doctor to override the programming but the Doctor tells him that the ship is being targeted by missiles and advises him to leave while he can. The trader assumes that he's bluffing but the Doctor opens the gate, tells the robots that Solomon wants to see them, and runs off with Rory and Brian.
As the Doctor runs away, he spots the triceratops and leaps aboard it, inviting Rory and Brian to join him. Meanwhile, the robots realize that they've been tricked and Solomon sends them after the Doctor. The Doctor is unable to get the triceratops moving and Brian throws another golf ball in front of the dinosaur. It runs off, losing the robots in the corridors, but the ball bounces off a wall and the triceratops skids to a halt, throwing off its passengers. The Doctor finds another computer console and Indira sends a message informing the Doctor that the ship is in the atmosphere and she has to activate the missile program. He asks for more time to preserve the cargo but Indira says that her only responsibility is Earth's safety and signs off to begin the missile launch sequence in thirty minutes.
Riddell finds a storage locker with Silurian weapons and Amy is shocked until the hunter reveals that they are stun weapons. Nefertiti is interested to know if the Doctor has a queen and Riddell suggests she pick a man of action with a larger weapon. They spot the Doctor on the internal monitors as Rory suggests they check the ship's weapon systems. The Doctor confirms there are no weapons and it's too late to get to the control deck. Solomon and the robots teleport in and the trader admits that Earth has launched missiles. As the triceratops wanders back, Solomon tells the Doctor that he has located Nefertiti and knows how valuable she is. He wants her in return for letting the rest of them live.
The Doctor refuses to negotiate and Solomon has the robots shoot the triceratops as an object lesson. As it lies dying, the Doctor goes to comfort it and Solomon warns that the robots will kill them all if he doesn't receive Nefertiti. Amy, Nefertiti, and Riddell teleport in and Nefertiti steps forward. She tells the Doctor that she is in his debt for saving her people, and Riddell threatens to shoots Solomon and the robots. Nefertiti tells him to let her make her own choice and he reluctantly lowers his weapon. Solomon slams Nefertiti against the wall, promising that he'll enjoy breaking her, and then teleports back to his ship with Nefertiti and the robots.
The ship's sensors detect the incoming missiles and the Doctor gets an idea. With seventeen minutes until impact, the Doctor heads for the control deck and explains that they need to turn the ship around.
Solomon tries to remove his ship from the ark and discovers that the Doctor has magnetized the hull, immobilizing them.
The baby Tyrannosaurs Rexes move in on the control deck and Riddell realizes that he's seriously outnumbered.
Indira and her people watch as the missiles approach the ark.
The Doctor discovers that the ship needs to be navigated by two individuals with the same gene chain. Brian points out that he and Rory are related and the Doctor has them sit in the command chairs. As the Doctor fiddles with the control, he asks Amy how her job is going and she explains that she gave it up because she was waiting for the Doctor to return. She points out that the gaps between his visits are growing larger but the Doctor assures her that he's not trying to get rid of her. As he finishes his rewiring, Riddell comes in and says he needs a second person, and Amy grabs a gun. The hunter is shocked and she assures him that she's worth two men, and the Doctor suddenly teleports away with a control circuit.
Amy and Riddell hold off the T-rexes with the stun guns.
Rory and Brian navigate the ark away from Earth as the missiles close in. However, the missiles are still locked in and will impact in seven minutes.
The Doctor teleports aboard Solomon's ship and short circuits the robots. Solomon threatens to kill Nefertiti if the Doctor doesn't release his ship, but Nefertiti knocks him down. The Doctor replaces the ship's signal with the Silurian ark, explaining that the missiles will follow it instead once he sends it off. He then puts the control circuit with the tracking signal down and prepares to demagnetize the hull. When Solomon offers him anything he wants, the Doctor asks if the Silurians begged him to stop before he killed them. He tells Solomon that the missiles are on the way and invites him to enjoy his bounty, and then leaves as the ship blasts away from the ark. The missiles change course and destroy Solomon and his vessel.
Amy and Riddell stand among a pile of stunned dinosaurs.
Later, everyone is ready to leave, but Amy and Rory ask the Doctor to take them home for a couple of months. Brian asks the Doctor for one favor and they are soon hovering above Earth as Brian enjoys the view of the planet from the door of the TARDIS.
Back in Africa, Riddell looks up at the sky, wearing a dinosaur fang around his neck. Nefertiti emerges from his tent, carrying a stun gun.
At home, Rory is working on the lights as they get postcards from Brian, who is traveling the world. They also get a postcard from the Doctor showing the dinosaurs and the TARDIS on the planet New Siluria.