Steven Moffat himself was pondering something big for the middle of the series - the destruction of the Earth, until he realised how that would impact future storytelling.
Moffat had then agreed to carry on Jamie Mathieson's idea of having the Doctor remain blind after the conclusion of his episode Oxygen.
The showrunner decided to bring these various threads together.
Basically, alien monks would almost bring about the end of the world, but usher in instead a dystopian Orwellian society. The Doctor's disability would - at least initially - prove a handicap to countering this threat.
Bill's role in events would be pivotal in the trilogy's development. It was also planned to make this the time to reveal who was in the Vault.
Moffat needed a starting point which he would write himself, and that's where this episode comes in...
Much of the episode is set in the Vatican's secret library - the Archivum Secretum. Part of the Vatican Library, it contains papal documents including letters to and from international leaders, as well as historic artefacts such as the trial record of Galileo, the Bull excommunicating Martin Luther, and Henry VIII's petition to have his marriage to Catherine of Aragon annulled.
It also contains documents regarded as heretical, and many believe that it holds secret evidence which would actually undermine the Vatican's authority - or even destroy the very foundations of Christianity, deliberately suppressed.
This takes us into Dan Brown territory. He has written a number of potboiler thrillers, some made into movies starring Tom Hanks, which were themselves inspired by supposedly factual books written by - amongst others - the co-creator of the Great Intelligence and the robot Yeti.
A court case cleared Brown of wilfully plagiarising The Holy Blood and the Holy Grail, a 1982 work by Michael Baigent, Richard Leigh and Henry Lincoln, despite The Da Vinci Code (2003) clearly being inspired by its hypothesis - namely that Jesus had a child with Mary Magdalene and eventually founded the Merovingian dynasty. The Vatican allegedly knows all this but suppresses it, but it is knowledge preserved by a secret society known as the Priory of Sion.
Instead of a murder in a museum triggering a story, here we have a bizarre suicide in a library - which turns out to be one of a series of similar deaths. All are people who have read a book - the Veritas.
The story's title Extremis can mean "at the point of death" (Missy's execution and the "deaths" of the virtual Doctor and companions), or to refer to an extremely difficult situation - something pushed to its furthermost limit.
Another literary inspiration, involving murder in an ecclesiastical library and the suppression of secret knowledge, is Umberto Eco's 1980 novel The Name of the Rose. This has also been adapted for cinema (1986) as well as a 2019 TV mini-series.
Whilst Presidents and Prime Ministers were fair game in drama, Moffat was concerned about the inclusion of the Pope in the episode, not wishing to cause offence, and he actually had the BBC clear this in advance. Whilst scenes involving the fictitious Pope are humorous, he is not himself made a figure of fun. Unlike other figures of authority over the years, the Doctor shows him respect.
The Doctor claims to have known Pope Benedict IX, who was Bishop of Rome in 1045. Benedict - real name Theophylact of Tusculum, reigned three times between 1032 and 1048. One of the "Bad Popes" he was deposed, resigned and sought to enrich himself from the position - even selling the Papacy at one point.
His life was reputedly one of scandal, including murder, rape and sodomy. He may possibly have been the youngest ever Pope, as one record claims he was only 11 or 12 when he ascended the Papal throne, though others claim he was aged 20.
A woman was alleged to have become Pope in the 9th Century, known as Pope Joan. This story only surfaced in the 13th Century and is believed to be pure fiction.
She was only found to be a woman when she gave birth during a procession, and future Popes avoided the spot where this was supposed to have happened. Belief in her existence was such that, until 1600, she had a statue amongst all the other Popes in Siena Cathedral. It was remodelled to make it masculine.
A ritual was created to ensure that no other woman could ever become Pope. During their coronation, an official would physically check their genitalia on a special chair.
One other area Moffat wanted to include in the episode was the notion of reality being an artificial construct. This had featured in several scientific and philosophical theories, but became famous through The Matrix film franchise.
Basically, we are all living in a Virtual Reality simulation, and occasionally there are glitches which reveal this fact.
The VR reveal takes place at CERN - the European Laboratory for Particle Physics. The organisation behind it was founded in 1954 and it was originally based at the University of Copenhagen under Niels Bohr. It later moved to Switzerland. It is best known for the Large Hadron Collider - a circular tunnel 27km in circumference, inaugurated in 2008. Some people at the time believed that it would create a Black Hole and destroy the planet. (Its opening was marked by a BBC radio Torchwood drama).
Moffat's son Joshua had just served a summer internship at CERN prior to studying Physics at university.
The oval-shaped doorways to other simulated locations were based on the video game Portal.
Nardole likens this to the Holodeck in Star Trek: The Next Generation, which was based on an episode of the animated series.
The story ends with a confrontation between the Doctor and one of the Monks in the Oval Office in the White House - a location which had featured prominently in The Impossible Astronaut / Day of the Moon.
The idea that a would-be invader might use a simulation as a precursor to invasion goes back at least as far as the Cold War. It was claimed that fake English villages were built behind the Iron Curtain to train spies.
This crops up in a number of TV dramas, such as Danger Man and The Avengers.
In Doctor Who we had seen it most notably in The Android Invasion, where the Kraals create a mock-up village of Devesham to test out their androids.
Before the Flood, just the season before this one, had been set partly in a fake Russian village in a Scottish valley in the 1980's.
After considering various characters such as Davros for the Vault inhabitant, Moffat had quickly decided on it being Missy. He knew that the mystery could not be sustained for the entire series, so opted to have her revealed at the mid-point. Moffat wanted to examine a new dynamic between her and the Doctor, which would feed into the later stages of the season. Missy is beginning to question her previous lifestyle and is apparently seeking redemption and a change from her evil ways.
The flashback sequences to the Executioners' planet also allowed the audience to see how Nardole came back into the Doctor's life - sent by his wife River Song. He has her journal - first seen in Silence in the Library / Forest of the Dead.
It is said that Time Lords have three brain stems, which confirms Missy's advice that Kate Stewart use two additional snipers in The Magician's Apprentice.
She claims to have known about the Doctor's retirement to Darillium from the Daleks - referencing both The Husbands of River Song and The Witch's Familiar.
Next time: the Monks set up a pyramid scheme, and we learn of the dangers of going to work with a hangover...
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