Queen Nefertiti and The Doctor

While visiting Queen Nefertiti, in 1334 BC Egypt, The Doctor receives a call from the Indian Space Agency in 2367 AD about a vast spaceship which will crash into Earth in six hours. The ISA plans to destroy it with missiles unless The Doctor can stop it first.

Taking Nefertiti with him, he picks up Edwardian explorer John Riddell from the African plains in 1902 A.D., and his companions Amy and Rory ten months after he last saw them in "Asylum of the Daleks" - inadvertently taking Rory's father Brian into the TARDIS as well.

When the TARDIS materialises in the spaceship they find that it contains loose dinosaurs, when two Ankylosaurus come out of the lift. Hiding as the dinosaurs go past, The Doctor keeps John Reddell from trying to harm them as they need to be preserved. The Doctor then discovers an interactive monitor which enables him to use the spaceship's computer to locate the engines, accidentally transporting himself, Rory, and Brian to the engine room, which appears to be a beach. The spaceship uses wave energy to generate endless power, hence the beach and sea. It is also used as a habitat for pterodactyls which attack The Doctor, Rory and Brian forcing them to take refuge in a cave in some nearby cliffs.

Riddell

There they encounter two comically clumsy robots who escort them to the only human on board, a brutal man called Solomon who is in a smaller spaceship that has docked with the larger spaceship. However, Solomon only allows The Doctor inside, leaving the two robots to guard over Rory and Brian. The Doctor finds Solomon has been injured in a raptor attack and has been waiting for a doctor to help him. Understanding Solomon's mistake, The Doctor asks him why he should help him. In response Solomon orders one of the robots to give Brian a painful laser burn as a warning. This forces The Doctor to work on getting Solomon mobile again while Rory tends to his father's burn.

Meanwhile Amy discovers that the spaceship is a Silurian Ark designed to carry the reptilian humanoids to a new planet along with flora and fauna from their time period. It left Earth millions of years ago to escape the meteor impact that wiped out the dinosaurs. Amy also discovers that the ark now registers zero Silurian life forms on board - The Doctor deducing correctly that Solomon might be responsible.

Brian Williams

Solomon reveals himself to be a lawless exotic black market trader who has raided the ark and killed the Silurians in order to steal the dinosaurs. Solomon insists that everything and everyone has a price. However, having had the robots murder all the Silurians, Solomon was unable to take control of the ark himself and the computer defaulted to return the ark to its point of origin - Earth.

Solomon is surprised when The Doctor does not appear in his databases. Despite being told about the ISA missiles the greedy Solomon believes The Doctor is lying and wants the dinosaurs for himself. The Doctor though manages to escape by tricking the robots guarding Brian and Rory. Finding another triceratops, The Doctor, Brian and Rory board it and toss one of Brain's golf balls to make it run from the robots. They succeed in getting away, but have a hard landing. The Doctor then receives a message from the ISA, saying that the missiles will be launched, despite his protests that the ark can be piloted away with its precious cargo.

Solomon then arrives by teleport, with his clumsy robots, and discovers Queen Nefertiti's identity and value. He decides to kidnap her and leave in his own spaceship. Solomon shows how far he is willing to go to achieve this by having his robots kill the triceratops and threatens to do the same to The Doctor's companions unless Queen Nefertiti is brought to him. Though The Doctor refuses, Queen Nefertiti agrees to go with him to save the others, despite Solomon's obvious sadistic intentions towards her.

Exploring the Spaceship

While Amy and John Riddell shoot hostile dinosaurs with tranquiliser shots, The Doctor disables Solomon's robots and rescues Queen Nefertiti – who has knocked Solomon down and has pinned him to the ground with his crutch after he insults her. The Doctor then tells Solomon that the ISA have launched missile towards the Silurian Ark and that they are locked onto the signal that is emanating from an orb that he then places in Solomon’s spaceship. The Doctor, with Queen Nefertiti, then teleports off of Solomon’s spaceship leaving him screaming in terror as his spaceship takes off and is hit by the missiles, exploding.

Meanwhile, Rory and Brian manage to pilot the Silurian Ark - The Doctor having previously explained that it can only be piloted by two who share the same DNA and this is the reason why Solomon could not control the ark. Rory and Brian manage to pilot the ark away from the Earth and into the emptiness of space.

The Doctor then takes Amy, Rory and Brian back to their home after letting Brian view the Earth from orbit. Queen Nefertiti, who has been flirting and clashing with the very macho John Riddell, opts to go with him rather than return to her own time.

A short time later Amy and Rory receive a series of postcards from all over the world sent by the previously travel-shy Brian. They also receive one from The Doctor, who has just visited the planet Siluria where the dinosaurs now reside.