The Doctor takes Clara and Courtney to the Moon in the year 2049. However, Astronauts are there to destroy it, as it appears it’s become dangerously unstable.
They soon discover why things are so weird-the moon’s gained additional mass, and nasty spider-monsters have invaded and killed a local base, as well as several of the astronauts.
Investigating further, the Doctor discovers the shocking truth-that the moon is in fact, a kind of giant egg with a creature gestating inside, and the spider-creatures are some kind of antibodies. This makes the astronauts even more insistent to destroy the moon, but Clara and Courtney are unsure. Wanting mankind to make the decision, the Doctor abandons Clara and Courtney, having them decide to ask the population of Earth about the fate of the moon and the creature inside.
Humanity votes to destroy the moon, but Clara decides to not destroy it at the last minute, and the Doctor picks her, Courtney, and the surviving astronaut off the moon as the moon ‘hatches’. On Earth, they witness some sort of space dragon emerge, and lay a new ‘egg’ moon.
Clara is very upset about being put in that whole situation, and wants to leave this new more callous Doctor. However, she agrees to one more trip. Courtney decides this whole thing is too much for her and leaves.
The Doctor and Clara then go to a spaceship modeled after the orient express. On the spaceship, people are dying 66 seconds after witnessing a mummy appear that only they can see.
The AI on the ship, Gus, is attempting to capture the Mummy for some reason, and has gathered many of the passengers-mostly scientists-onboard the ship so they can capture it for his benefactors and reverse-engineer it. The Doctor eventually figures out that the Mummy is a stealth soldier from some war, and convinces it that it’s mission is over.
Gus tries to destroy the ship and kill the Doctor and the passengers, but the Doctor is able to save the survivors with a teleportation device and the TARDIS. Clara decides she still wants to travel with the Doctor after all….