The whole party flee through the spaceship, eventually hiding in an alcove. Riddell wants to kill the dinosaurs but the Doctor tells him they are there to preserve them. Rory wonders whose space ship it is. Unknown to them, they are being observed on a screen somewhere within the ship. Brian asks if the dinosaurs are flying the space ship. The Doctor replies that would be ridiculous; they are probably passengers.
The Doctor, Brian and Rory locate a screen that allows them to look at the ship's systems. The Doctor mentions that they need to get to the engines. All three of them promptly find themselves on a beach. Brian loses his temper with the Doctor and demands to know where they are. Rory explains that his dad is a nervous traveller, who only goes to golf and the paper shop, while the Doctor sticks out his tongue and tastes the air. He says that it is too metallic to be Earth. Rory notices that the beach is humming so the Doctor tells them to dig while he looks at the rocks. Brian produces a trowel from his pocket ("What sort of man doesn't carry a trowel?") and digs down to find a metal floor beneath the sand.
The mysterious observer notes that Rory shouted "Doctor!" and demands the newcomers brought to him.
Amy tells Riddell to stop drinking from his flask. He says that he doesn't take orders from females but Nefertiti says if he speaks to her that way then she will have him executed. Amy asks her who she is and, learning she is the queen of ancient Egypt is duly impressed. Nefertiti asks if Amy is a queen. She replies that she is Rory's queen but not to repeat that to him. It is then that they realise they have blundered into a T.Rex nest. They tiptoe away.
The Doctor is overjoyed to find a screen in the rocks that tells him they are still aboard the ship and that it is powered by the waves. The problem is that it will take too long to shut down the engines. Added to that, a flock of pterodactyls is closing in. The three of them run to the safety of a cave. This turns out to be the entrance to a tunnel down which two large robots are coming. The robots say they are very cross with the Doctor. They lead him and his party through the ship, letting slip that they have been aboard for two thousand years. On the way they meet a triceratops which is very affectionate towards Brian. He gets rid of it by throwing a golf ball for it to chase.
Amy finds a screen and accesses the ship's data records. She learns that she is aboard a Silurian ship, built to take a cohort of people, in cryogenic suspension, away from the predicted impact of an asteroid on Earth. It is an arc, carrying fifty species of animals, too. Riddell asks where the Silurians have gone. Amy uses the computer to find that they have apparently left the ship. When she looks to see what has changed since the ship set off she finds another ship is aboard.
This is where the Doctor is led to. He enters a room where Schubert's "Fantasia" is playing. He comments that he played on this piece. He finds an injured old man called Solomon who assumes he is a medical doctor able to heal his legs after an encounter with three raptors. The Doctor says that he will repair Solomon's legs if he explains where he got the dinosaurs from. Solomon's response is to tell the robots to injure Brian. One of them shoots him in the shoulder. Solomon says that he doesn't like questions and if the Doctor doesn't heal him the next shot will be fatal. Rory uses some medicine he picked up on his travels to heal Brian. Amy rings him and tells him to let the Doctor know that they are on a Silurian vessel.
Solomon says that he acquired the ship and is transporting it to the Roxborne Peninsula, a commercial colony. The Doctor realises that a purple light that scanned him was to see who he was and how much he was worth. However, the result is that the Doctor apparently doesn't exist, the first time this has happened, says Solomon.
Just as the Doctor finishes fixing the old man's legs, Rory passes his phone through. Amy tells him what she has found out. The Doctor asks Solomon what happened to the Silurians. Solomon says that the robots woke them a handful at a time while he offered them a price for the dinosaurs. When they refused to sell they were ejected into space, thousands of them. The Doctor wonders why a ship going to the Roxborne Peninsula is heading for Earth. He then realises that the ship set a course for home when its crew left and Solomon can't over-ride it. He adds that the ship is targeted by missiles but Solomon is sceptical.
The Doctor leaves the room, telling the robots that they are wanted inside. He takes Rory and Brian to the triceratops and leaps on its back. Brian throws a golf ball for it to follow and they make their escape while the robots follow very slowly, shooting inaccurately. The triceratops deposits them near some screens where an incoming message from Indira tells them that they are entering the earth's atmosphere and the missiles are about to be launched.
Riddell finds some tranquiliser guns. He begins to partake in some crude flirting with Nefertiti. Elsewhere, Solomon and the robots arrive beside the Doctor. Solomon believes in the missiles but realises he will have to leave on his own ship which means losing the dinosaurs. However, he plans to take Nefertiti instead, since his IV device has told him who she is and how much she is worth. The Doctor refuses to hand her over but to prove his ruthlessness Solomon has one of his robots kill the triceratops. This whole encounter has been watched by Amy and her group via a screen. Nefertiti demands to be teleported in with her friends and hands herself over to Solomon.
The Doctor and Riddell try to stop her but she is determined, even when Solomon makes suggestive remarks. He teleports, with her, back to his ship. The Doctor accesses the controls and magnetises Solomon's ship so that he can't escape. However, he needs two people from the same gene chain to steer the Silurian ship away from Earth. Brian points out that he and Rory can do the job. While they take the controls, the Doctor and Amy work on the machinery. As they do, they talk. Amy says that she can't settle to anything in her life: she is always worrying that the Doctor will never return. He says that she will, outlive him but when she says it could be the other way round he gives her a meaningful look and kisses her forehead. The Doctor removes a green cube from the controls while Amy and Riddell step outside with guns to hold off a raptor attack.
Brian and Rory exultantly steer the ship away from Earth but the missiles are still locked on. The Doctor teleports onto Solomon's ship and incapacitates the robots. He tells Solomon that the missiles are locked onto the cube which he places on a table. Solomon threatens to kill Nefertiti but she overpowers him, saying she is nobody's possession. The Doctor tells Solomon to look at the missiles and think how valuable they are; he adds that they are all Solomon's. The Doctor leads Nefertiti back to the Silurian ship and releases the magnetic clamps. Solomon's ship breaks away and is destroyed by the missiles.
The Doctor says it is time to drop the dinosaurs off but Amy and Rory say that they would rather go home for a couple of months. Brian asks a favour before that. There is a cut to a shot of the TARDIS orbiting the Earth while Brian sits in the doorway, looking at the planet below. Amy and Rory join him while the Doctor stands behind, looking at them wistfully.
Back on the African plains, Riddell looks up at the stars. Nefertiti steps out of his tent, holding a rather large Silurian weapon.
Rory tries to fix a light bulb. Amy enters with another postcard from Brian. She puts it beside other cards from Rio, Pisa and the Taj Mahal. The new card shows a picture of the TARDIS and some dinosaurs and is labelled "Siluria".
