The year is 2119, and the crew of an underwater mining facility discover a spacecraft.
While investigating the ship, a strange marking is found on the interior wall. Suddenly, an entity fires up the engines causing the captain to push one of his crew to safety. Unfortunately, Captain Moran dies and moments later his "ghost" materializes.
Three days later, the TARDIS delivers The Doctor and Clara to the base. While she is craving adventure, the Doctor senses his time machine is unhappy.
The pair come across the ghosts, who at first don't harm them but rather lead them to the ship. The Doctor spots the alien writing and finds it curious the TARDIS has not translated it. At that point, the ghosts arm themselves and attack our heroes.
Making a run for it, the Doctor and Clara come across the remaining crew locked in a room. "Tell me, what about those things out there? What are they? Why are they trying to kill us?" the Doctor demands. "Well, they're... they're ghosts" Bennett replies.
Refusing to believe the entities are ghosts, the Doctor questions the survivors. They share their story and inform him that for some reason the ghosts can not enter the Faraday Cage. Bennett gives a little more history, explaining they are sitting in a valley that was flooded when a dam burst.
The computer switches the lights on, advising it's morning. The ghosts are nocturnal.
"So we are fighting an unknown homicidal force — that has taken the form of your commanding officer and a cowardly alien — underwater, in a nuclear reactor. Anything else I should know?" the Doctor asks.
He soon notices that a suspended animation chamber and power cell are missing from the alien ship. O'Donnell swears the crew has not moved a thing off the mysterious vessel, they simply haven't had time. Pritchard, however, takes an interest in the power cell and goes in search of it.
The Doctor comes to the conclusion they are dealing with ghosts. Clara's confused.
Pritchard's greed gets him killed by Moran's ghost, adding another member to their ranks. O'Donnell manages to switch the base to morning mode, and when the lights come on the ghosts vanish.
When Cass decides their best chance of survival is to abandon the base, they learn a submarine was already on its way. The ghosts, via morse code, attempted to bring more bodies to the base. The Doctor warns those at the surface to stay clear, the base is now under quarantine.
The Doctor needs more information, so he asks O'Donnell to switch the base back to night mode. Using the crew as bait, they draw the ghosts inside the Faraday Cage. The Doctor joins them inside and using his sonic shades allows Cass to read their lips.
"The dark. The sword. The forsaken. The temple" Moran's ghost mouths.
It turns out, these are coordinates which lead to a church outside the base. The Doctor realizes the ghosts are not a natural phenomena. "It means that someone is deliberately getting people killed, hijacking their souls and turning them into transmitters" he tells everyone.
Using a miniature sub, the group discovers the suspended animation chamber at the church site. They can not open it. More questions.
The Doctor decides to go back to before the flood for some real answers.
Wondering if the Doctor won't just abandon them, Clara tells the crew "He's gonna go away, come back and we'll have to listen to how he did it." Moments later, she spots a ghost Doctor floating outside the base.