While in 1334 BC Egypt with Queen Nefertiti, 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 stops it first. Taking Nefertiti with him, he picks up Edwardian explorer John Riddell from the African plains in 1902 AD. He then materialises the TARDIS around his companions Amy and Rory ten months after he last saw them in "Asylum of the Daleks", inadvertently taking Rory's father Brian on the TARDIS as well. They materialise in the spaceship and find that it contains dinosaurs.
When asking the ship's computer for the engines, the Doctor, Rory, and Brian are transportated to the "engine room", a large beach on the ship which uses the waves as hydro-power. Meanwhile, with Nefertiti and Riddell, Amy discovers that the ship 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. The ship, however, registers no Silurian life forms left on board. After escaping from a group of pterodactyls, the Doctor, Rory, and Brian are escorted by two robots to the only human on board, a brutal man called Solomon who has been injured in a raptor attack and requires medical help. Scanning the Doctor to see who he is, Solomon is surprised that the Doctor does not appear in his universal database. Solomon reveals himself to be a lawless exotic black market trader who has raided the spaceship in order to steal the dinosaurs. Having had the robots murder all of the Silurians, Solomon was unable to take control of the ship himself and the computer defaulted to its point of origin, causing it to return to Earth. Discovering Queen Nefertiti's identity and value, he decides to kidnap her and leave in his own ship. Though the Doctor refuses, Nefertiti agrees to go with him to save the others, despite the man's obvious sadistic intentions towards her.
While Amy and Riddell shoot hostile dinosaurs with a tranquiliser gun, the Doctor disables Solomon's robots and rescues Nefertiti, then tricks the ISA missiles into targeting Solomon's ship rather than the ark: it is destroyed, taking him with it. Rory and Brian pilot the ark away from the Earth, as the ship can only be piloted by two people of the same gene pool. The Doctor then takes Amy and Rory back to their home after letting Brian view the Earth from orbit. Nefertiti, who has been flirting and clashing with Riddell, opts to go with him rather than return to her own time. Amy and Rory receive a series of postcards from all over the world sent by the previously travel-shy Brian, along with one featuring the dinosaurs, the TARDIS, and a sign saying "Siluria".
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