In 2119, the Drum underwater mining facility sits on the bottom of a Scottish lake near a submerged town, from which a spaceship has been recovered. Captain Moran dies after observing strange symbols carved into the vessel's hull... and then reappears as a hideously distorted phantom, mouthing silent words. When the TARDIS arrives, the Doctor and Clara discover that a second ghost has joined Moran, and they are trying to add to their ranks by killing the Drum's remaining personnel. The Doctor realises that the truth about the spectres lies in 1980 -- in the hours before the town was drowned -- with the terrible Fisher King.

Although Doctor Who had often sought inspiration in classic horror stories, only rarely had it featured entities of a ghostly nature. Perhaps the two most prominent examples of Doctor Who phantoms had been the Gelth of 2005's The Unquiet Dead, which had turned out to be gaseous aliens seeping through a rift in time and space, and Hila Tacorien, the lost explorer trapped in an extra-dimensional space in 2013's Hide. For Season Thirty-Five, executive producer Steven Moffat wanted to pit the Doctor against ghosts in their most familiar form: as the revenant spirits of the dead.

A natural candidate to write such an adventure was Toby Whithouse, who had drawn upon various supernatural traditions for his successful drama Being Human. Whithouse had most recently contributed A Town Called Mercy to Doctor Who's thirty-third season, since when he had been occupied on other projects. However, he confirmed to Moffat that he would be able to make room in his schedule for a new Doctor Who script during the latter part of 2014. These plans were nearly thrown into disarray when Whithouse learned that Season Thirty-Five was being structured to consist primarily of two-part stories. He was uncertain about his ability to commit to a pair of scripts, but he finally relented when he was informed that his adventure would be made first, and hence would have few budgetary constraints. In the transmission order, it would ultimately comprise the year's third and fourth episodes.

The presence of a Faraday cage was inspired by one of Toby Whithouse's unused Being Human concepts

The ghost story was one of two ideas that Moffat suggested Whithouse might pursue. For his part, Whithouse had been considering the notion of a curse which passed from person to person, deriving its power from an alien lifeform which inhabited the words themselves. Moffat liked this concept, and he suggested that it should be incorporated into the narrative about the phantoms. Whithouse also wanted to try his hand at an adventure which played with paradoxes and time travel, elements which Moffat had often included in his own scripts. To prevent the ghost story from descending too far into cliche, it was agreed that the setting would be a futuristic base; a space station or a moon outpost were discussed, before it was noted that Doctor Who had only rarely taken place in an underwater facility. The presence of a Faraday cage was inspired by research which Whithouse had undertaken for an ultimately-unused Being Human concept.

Moffat believed that two-part stories worked best when the second installment diverged in some significant way from the opening episode. As such, Whithouse decided that the storyline would open up beyond the underwater base in the second script. Having long been intrigued by remote military outposts, of the type featured in 1989's The Curse Of Fenric, he chose a deserted army installation as the new setting. The second episode would also introduce the villain of the piece, whom Whithouse dubbed the Fisher King. This name was borrowed from Arthurian mythology, in which it was applied to a guardian of the Holy Grail.

The notion of the ghosts mouthing silent words led Whithouse to develop a character who could read lips. This became Cass, a deaf woman, whose inclusion was partly a response to a call for greater diversity and representation in British television and film. Whithouse decided to revisit the Tivolians, whom he had created for 2011's The God Complex, since their subservient attitude seemed appropriate for a race which had been conquered by the Fisher King. The Arcateenians, liberators of Tivoli, had also debuted in an earlier Whithouse script: Greeks Bearing Gifts, a 2006 episode of the spin-off series Torchwood.

By the time the first draft of episode one was completed in late September, Whithouse's adventure was called “Ghost In The Machine”. At this stage, Moran was called Hicks, while Prentis' phantom was absent. Episode two, written by mid-October, initially revealed that O'Donnell's death was just a feint, and she and Bennett were reunited at the story's conclusion. This element was dropped to avoid over-complicating the time paradox.

Originally, the Doctor told a story about a time traveller who accidentally killed Leonardo da Vinci in infancy

A late change was to the fourth-wall-breaking explanation of a bootstrap paradox -- a scene which Whithouse was surprised to be allowed to retain at all. Originally, the Doctor told a story about a time traveller who accidentally killed Leonardo da Vinci in infancy, and used documents he had brought with him from the future to forge all of Leonardo's discoveries and accomplishments. Later, this became the Doctor's possession of a postcard of the painting The Last Supper, which in turn became the basis of Leonardo's genuine masterpiece. However, it was then decided to tie the scene into Moffat's introduction of the Doctor's electric guitar in the season premiere, The Magician's Apprentice / The Witch's Familiar. The subject of the monologue consequently changed from Leonardo to composer Ludwig van Beethoven.

With regular Doctor Who producer Nikki Wilson on maternity leave, Derek Ritchie was tapped to replace her for the early part of Season Thirty-Five, including the first recording block. Ritchie had produced the third season of Wizards Vs Aliens, having been a script editor during its first two years. He had also been a script editor on Doctor Who, responsible for the 2013 Christmas special, The Time Of The Doctor, and three episodes during Season Thirty-Four. Daniel O'Hara, with whom Ritchie had worked on Wizards Vs Aliens, was assigned to direct “Ghost In The Machine”; this would be his only Doctor Who story.

Amongst the cast was Sophie Stone, taking the role of Cass. The first deaf student ever admitted to the Royal Academy of Dramatic Art, she had appeared in programmes such as Marchlands. Zaqi Ismail, playing Lunn, had previously learned British Sign Language to facilitate communication with his deaf sister. Chosen to create the physical form of the Fisher King was Neil Fingleton. He measured ninety-one inches tall, which was acknowledged by the Guinness Book of World Records as an unprecedented feat for a British-born man. With the added height provided by the costume designed for Fingleton to wear, the Fisher King would stand more than eight feet tall.

Doctor Who resumed filming on January 5th, 2015, three months after the completion of the previous year's holiday special, Last Christmas. The first four weeks of work on “Ghost In The Machine” would be spent exclusively at the programme's usual production home of Roath Lock Studios in Cardiff. Sadly, Peter Capaldi's mother, Nancy, passed away on the 3rd, prompting her son to return to his native Glasgow to be with his family. As a result, O'Hara had to hastily rearrange his recording schedule so that the initial days were devoted to material in which the Doctor did not appear. A further complication arose during rehearsals when the actors playing the ghosts found themselves struggling with the black gauze which was meant to obscure their eyes. It was quickly agreed that this effect -- inspired by the make-up worn by Peter Cushing in the 1972 horror film Tales From The Crypt -- would instead be achieved using computer animation.

Roundels were added to the TARDIS set to echo the aesthetic which been predominant in the 20th century

In the event, the only material recorded on January 5th was of Bennett in the TARDIS. Production designer Michael Pickwoad had further modified this set to reflect the Twelfth Doctor's developing personality, with roundels having been added to echo the aesthetic which had been predominant in twentieth-century Doctor Who. The rest of the week, through to January 9th, largely focussed on scenes in the corridors of the Drum. The set for the Faraday cage was also in use on the 7th and 9th, and O'Hara recorded the effects shot of the alien symbols reflecting off Moran's and Prentis' eyeballs during the latter day.

Capaldi rejoined the production after the weekend, when January 12th and 13th dealt with additional sequences in the corridors and inside the Faraday cage. The rest of the week, from the 14th to the 16th, was spent on the set for the gallery, with O'Hara capturing an additional shot in the Faraday cage on the 16th. Morven Christie, playing O'Donnell, now found herself developing a dermatological reaction to the facial prosthetic she wore as a ghost. After various options were considered, it was agreed that Sarah Brazier, an actress who was similar in appearance, would be hired to portray O'Donnell's spectre.

The week of January 19th to 23rd was almost completely devoted to the large hangar set and the recovered spaceship which stood within it. Part of the last day also included filming on the bridge of the Drum. Although the production then stood down for the weekend, a special audio recording session took place on the 24th. Both O'Hara and Ritchie were fans of the American heavy metal band Slipknot, which was scheduled to give a concert in Cardiff that night. They knew that lead singer Corey Taylor had enjoyed Doctor Who since discovering Tom Baker's Fourth Doctor via the regular repeats of his episodes on the Public Broadcasting Service in the United States. One of Taylor's signatures was a distinctive stage growl, which was deemed to be an excellent basis for the Fisher King's roar. After his representatives were approached about the idea, Taylor accepted a private tour of the Doctor Who set prior to the concert, during which he provided various howls which would be edited to create the sound of the Fisher King.

More bridge material was taped on January 26th and 27th. The latter part of the second day saw O'Hara's team return to the Drum corridors; rather than the straight configuration used for the first week of the shoot, they had now been rebuilt to represent the curved sections of the passageways. The rest of the week, through to January 30th, largely concentrated on these sequences. Part of the 29th was spent on green screen footage of the ghosts, plus water and smoke elements. Also on the itinerary for the 30th was action in the airlock -- including a model version used for its flooding -- and more effects shots of the phantoms, such as the Doctor's ersatz spectre hovering in the water outside the Drum. The shots of the alien symbols reflecting off the Doctor and Clara's eyeballs were also captured that day.

The only week of location filming for “Ghost In The Machine” took place from February 2nd to 6th. The lone venue was MOD Caerwent, a training area where all of the 1980 scenes would be recorded. Amongst the work undertaken on the 5th were shots which would be used to create the footage of the unmanned submarine travelling through the submerged town.

It was back to Roath Lock for the final three days of principal photography, from February 9th to 11th, with the standing TARDIS set in use throughout. The Doctor's monologue at the start of part two was one of the last scenes to be taped. There had now been some misgivings about the Doctor speaking directly to the camera, with consideration given to showing Clara present to listen to the speech, but this idea was ultimately rejected. Capaldi himself had helped select the rare make of Yamaha guitar which would now be seen throughout the season. During recording pauses, he improvised his own rendition of the Doctor Who theme music, which O'Hara recorded and later incorporated into the opening title sequence for episode two. Other work on February 9th involved green screen shots of Pritchard's corpse floating through the water, and the ghostly Doctor entering the Drum via the window. A shot of the power cell at the base of the dam was captured on the 11th.

Finally, on March 27th, O'Hara returned to Roath Lock to tape pick-up shots in the TARDIS console room, plus additional water elements. By this time, the first episode had been renamed Under The Lake; around early May, part two was likewise given the revised title Before The Flood. Amongst the scenes deleted in editing was one in which Prentis explained that the Fisher King came from a very arid world. The amphibious Arcateenians defeated him by raising the sea level on Tivoli, flooding the cities which the Fisher King's armies had conquered. Also dropped was the explanation that the ghosts were powered by a planet's magnetic field, and that they couldn't manifest when the Drum was in Day Mode because the facility's automatic systems generated their own magnetic field, out of phase with the Earth's.

Under The Lake aired on October 3rd, with Before The Flood following on the 10th. Because its lead-in, Strictly Come Dancing, had now expanded to more than two hours' duration, Doctor Who was pushed back to 8.25pm -- forty minutes later than the preceding episode, The Witch's Familiar. Since The National Lottery: In It To Win It had ended its run the week before, Casualty now trailed Doctor Who in the Saturday evening schedules.

• Doctor Who: The Complete History #81, 2018, “Story 255: Under The Lake / Before The Flood”, edited by John Ainsworth, Hachette Partworks Ltd.