We open on The Drum, an underwater mining facility in Scotland in 2119. The crew is investigating a mysterious ship that has appeared on the facility, arguing over who it belongs to and wat to do with it. There's writing scrawled into the inside wall of the ship. The sip fires its thrusters, trapping Moran in the flames. Safety protocols are initiated, and the remaining crew leave the main hangar before it locks down. Outside, two ghosts – one Moran – await them.
We pick up three days layer. The TARDIS can be heard materializing on The Drum. The Doctor is outside, asking the TARDIS why it's unhappy. Clara is eager to keep moving on, but the Doctor wants to know why the TARDIS brought them there.
Clara and the Doctor investigate the Drum, which is in disarray an apparently abandoned. They continue into a hall, and find the ghosts, Prentis and Moran. The ghosts approach them and examine them up close before turning away. The Doctor and Clara follow the ghosts through the Drum, into the hangar with the mysterious ship. The Doctor notices the writing on the ship's inner wall, and notes that its odd the TARDIS hasn't translated it for them. Moran picks an ax up off the wall, and Prentis takes a harpoon. They attack the Doctor and Clara, but the Doctor and Clara run.
The Doctor and Clara hide in a hall, but the ghosts phase through to them. The Doctor and Clara run and find a room where the remaining crew are holed up. The crew lets them inside. The crew asks who they are, and the Doctor introduces himself with psychic paper which tells them he's with UNIT. The crew introduces themselves, and O'Donnell fangirls out a bit. The Doctor gets what information he can from the crew. Cass, using sign language, tells the Doctor that, the ghosts can't enter this Faraday cage. Cass says she's in charge, but Pritchard points out that his company owns the rights to the oil. The Drum's systems reboot as morning dawns. The crew exists the room, telling the Doctor that the ghosts only come out at night.
The Doctor, insisting the ghosts are not ghosts, asks why the crew haven't left yet. Pritchard explains there is too much money at stake. The Doctor calls him an idiot, and goes about investigating the ship further. He opens a pane in the floor, and then asks where the stuff they've taken out is. A power cell is missing from the ship, and so is a suspended animation chamber. Cass keeps Lunn out of the ship, saying it's not safe. O'Donnell says no one has taken anything out of the ship. The Doctor, with a startling amount of enthusiasm, explains that they're actually dead and now ghosts. The crew reminds the Doctor that Moran was their friend. Clara passes him a card to recite to express grief to them, but the Doctor can't hide his curiosity. The lights go out around the Drum as it suddenly reenters night mode.
The TARDIS begins making a sound and the Doctor and Clara run back to it. He realizes the TARDIS wants to get away from the ghosts, so he puts the handbrake on. Clara is eager to get back to the adventure, and the Doctor tries to tame her enthusiasm. She expresses appreciation, and they get back to it.
Pritchard comes back from an excursion outside to search for the missing power cell. He's greeted by the ghosts. Moran seems to be trying to say something to Pritchard, then opens the hatch to dump Pritchard outside without his helmet.
Bennett expresses his desire to work for UNIT to Clara. Everyone is looking for Prtichard, who suddenly appears in the room with Clara and Bennett. They then see Pritchard's body float into the window outside. Pritchard turns to show his ghostly visage as the Doctor and other crew members arrive. Pritchard grabs a chair to attack just as O'Donnell turns the day mode on.
The Doctor tells them that the ghosts are learning to use the base against them. Cass says they abandon the Drum. The Doctor and Clara plan to investigate further. O'Donnell makes a call for a rescue sub only to find that a rescue request has already been made. The Doctor grabs the phone and tells them to send the submarine back, and that the Drum is under quarantine. He figures the ghosts ordered the ship with Morse code because they want off the Drum. The Doctor tells O'Donnell to the Drum back into night mode so they can figure out what these ghosts want.
Bennett draws out the ghosts. The Doctor gives Clara instructions on where to lead them. She leads them on the chase towards Lunn, who will lead them to a room with a flood door. The ghosts split up. Moran and Prentis follow Clara, while Pritchard chases Lunn. Clara finds a flood door and hides behind it. Lunn does the same, but Pritchard saw him go in and follows. Pritchard gets close to Lunn, grabs a large wrench off the wall, then leaves, dropping the wrench behind him.
The other two ghosts are around the corner from Bennett. He leads them out again, and Pritchard joins the chase. They see a hologram of Clara in the Faraday cage, and go inside after her. The door is closed behind them. Cass says she can't see the ghosts through the glass. The Doctor, now just outside the room, has them open the door so he can go inside. Moran puts a hand in the Doctor's chest, but he is unimpressed. Looking through the Doctor's sonic sunglasses, Cass reads the ghosts' lips. There are all repeatedly saying "the dark, the sword, the forsaken, the temple."
The Doctor realizes that the message is coordinates. "The dark" means space. "The sword" is Orion's sword, hanging from his belt. The fourth part of the sword is the Earth. "The forsaken" are the dead they're using to resonate and send they're message further. The Doctor realizes this means someone is doing purposely. Cass asks what the "the temple" is, and the Doctor says it's the church in the city outside the Drum. Whatever the coordinates are pointing to is in that church. The Doctor gives them the choice to stay or leave. Cass says she'll stay, that it's her responsibility. The rest of the crew follows suit.
The Doctor, Clara and the crew send a drone sub out to investigate the city. Bennett pilots and finds the church. There, they find the suspended animation chamber that was missing from the ship. The Doctor says the ship's pilot should be inside, but he has a feeling it isn't. He reexamines the markings inside the ship, wondering why they're not translated. He asks Cass what's the weirdest thing about all of this. She says the markings. He says they're not just words, they're magnetic forces that rewrite the synaptic connections in their brain. They're embedding the coordinates into their brains, so they keep humming it even after they die, while whatever put the message there slumbers in the suspended animation chamber.
A computer malfunction causes the Drum to begin flooding. The Doctor leads the crew towards the TARDIS. Flood doors shut along the way, trapping O'Donnell and the Doctor and half the crew on one side, and Clara and the rest on the other side. The Doctor tells Clara he's going to go back in time to when the spaceship landed so that he can understand what's happening. The TARDIS embarks, and Clara, Cass, and Lunn see another ghost outside. It's the Doctor.