In the near future, the Doctor and Clara find themselves on a space shuttle making a suicide mission to the moon. Crash-landing on the lunar surface, they find a mining base full of corpses, vicious spider-like creatures poised to attack and a terrible dilemma. When Clara turns to the Doctor for help, she gets the shock of her life.
After the events of “The Caretaker”, Clara Oswald warns the Doctor that her student, Courtney Woods, is still interested in his TARDIS and is trying to clean up the mess inside it she made previously. As they enter the TARDIS, the Doctor stops Courtney from cleaning and offers to take her and Clara on a trip in the time machine.
They arrive in 2049 on a space shuttle filled with nuclear devices on crash course with the Moon. They survive the crash and while the Doctor is curious about the higher-than-expected gravity, they are met by three astronauts. Their captain explains they are on a suicide mission to blow up the Moon; she explains that years earlier, there was a sudden mass high tide, wiping out a significant fraction of humanity and taking out many of Earth’s artificial satellites. Mankind abandoned scientific advancement for the sake of the survival of the species, a decision with personal consequences for the captain, Lundvik, whose space ambitions were thwarted as a result. A Mexican lunar colony reported changes in the Moon before Earth lost contact with them, leading scientists to conclude whatever caused Earth’s problems originated on the Moon. By destroying the Moon, they hope to save Earth from further devastation. Clara privately asks the Doctor about this point in time, having witnessed the continued presence of the Moon at later points in time. The Doctor reveals this to be a moment where time is in flux: he cannot “see” what happens.
The group sets for the Mexican colony, which they find covered in webbing. Captain Lundvik sends one of the crew members to prime the bombs as they explore the colony; he is attacked on the way back when he investigates an opening on the surface. In the colony, they find the colonists entombed in more of the webbing. The Doctor reviews the readings taken by the colonists, showing seismic activity on the surface and an increase of the Moon’s mass by over one billion tons, explaining the sudden tidal shift on Earth. A spider-like creature attacks them, killing Lundvik’s other astronaut. Courtney kills the creature using disinfecting fluid she brought to use in the TARDIS earlier. The Doctor realises these creatures are like germs, and after returning Courtney to the safety of the TARDIS, leads the group back outside to investigate one of the cracks on the surface. They find thousands more spider-like creatures inside the crack, and the Doctor discovers amniotic fluid nearby. To the others’ surprise, the Doctor tells them he will be back and dives into the hole.
Clara and Lundvik witness the Shuttle fall into a crack on the surface, and return to the colony to wait, with Lundvik preparing to set the timer on the nuclear detonators despite Clara’s assurance the Doctor will be back. The Doctor appears soon after and brings the TARDIS to the colony, where Courtney is still safe. The Doctor explains that the Moon is really a 100-million-year-old egg, the creature inside ready to hatch, and the spider-like creatures the equivalent of microbes on the surface of the egg. Lundvik immediately asserts that they should still destroy the Moon and kill the creature in order to prevent any possible harm to humanity the creature may cause, but Clara refuses to accept this solution and turns to the Doctor for advice. Addressing them as “Womankind”, The Doctor tells them this is a decision for the human race to make without his interference and departs in the TARDIS, leaving them to decide the fate of the creature in the egg in the time it has to hatch, about an hour and half.
As time passes, Clara, Courtney and Lundvik cannot reach a consensus. As the creatures begin to swarm the surface, Lundvik is able to make contact with Earth, and Clara uses a simultaneous television broadcast to plead with humanity to help them make their choice, by either turning off their lights to destroy the Moon or keeping them on to let the creature live (a scene shown in medias res at the start of the episode). Lundvik then initiates the countdown on the nuclear devices as they wait for Earth’s response which they will be able to see from the Moon. The lights on Earth go out, but Clara intervenes and stops the countdown. At the last moment, the Doctor returns, knowing they have decided to allow the creature to live, and rescues them from the Moon as it starts to crumble.
Back on Earth, the four watch as the winged creature hatches and flies away, the shell of the Moon harmlessly disintegrating. At Clara’s insistence, the Doctor reveals that because of the brief re-interest in what happened with the Moon, humanity would be re-inspired to travel to the stars, helping them to spread across the universe, and then assures Lundvik that she will now have a real space programme to lead. They then witness a new Moon – a freshly-laid egg by the creature – appear in Earth’s orbit. Later, alone with the Doctor, Clara angrily confronts him about having forced her to participate and finally make that choice, telling him that having made himself a friend to humans (he walks the Earth and breathes its air), he is not above them. She tells him that she does not want to see him again. After she leaves the TARDIS back at Coal Hill, she is comforted by Danny Pink. She explains to him that she is done with the Doctor but Danny thinks that she is really not ready to move on. When asked how he became so wise, we learn that he left the army under circumstances that he refers to as a “really bad day”. Later that evening, Clara returns to her flat and looks out her window at the Moon.