Mark Gatiss becomes the first writer (after the showrunner himself) to write for the new set-up. He and Moffat will form a successful writing partnership which will include Sherlock and an adaptation of Dracula.
Moffat wished to follow the now common practice of having seasons commence with a contemporary story, followed by a futuristic one, and then a historical.
Gatiss' previous stories had been set in relatively recent historical periods - the Victorian era and the 1950's. His work for the Virgin and BBC book ranges had also tended to have similar historical settings.
This time round, he opts for World War II. This is the season's Celebrity Historical, so he opts for the inclusion of wartime Prime Minister Winston Churchill.
The WW2 setting saw Gatiss revisit childhood memories of classic British war movies. Two in particular stand out - Where Eagles Dare (1968) and The Battle of Britain (1969).
From the first we have the Spitfire call signs "Broadsword calling Danny Boy" - you can almost hear Richard Burton saying it - whilst the Spitfire dogfight and images of the RAF Fighter Command centre, with models pushed about a map, come from the latter.
Gatiss himself, who previously acted in the series, gave voice to the Spitfire pilot.
The Daleks were redesigned for this story - supposedly a new permanent variation on the design. The larger size and colourful nature of the "New Paradigm" derived from the Aaru Dalek movies which had starred Peter Cushing as Dr. Who. Moffat had already used the cinematic TARDIS as inspiration for his new Police Box exterior.
The cinema Daleks had had different ranks, indicated by colour (black, gold, red). Gatiss and Moffat went for both rank (the white Supreme) and function.
The plan was that they would have an equipment hatch at the rear of the casing from which different appendages could emerge, rotating round the groove which runs round the middle section.
Unfortunately this simply resulted in them looking hunch-backed, their graceful symmetry destroyed.
Instead of metallic colouring, they looked like they were now manufactured from plastic. Fans likened them to Tele-Tubbies, or to colour-coded household recycling bins which were then proliferating.
Daleks had always been likened to armoured tanks, and this image was accentuated by having the RTD design props repainted in military khaki camouflage colours, with webbing accoutrements - and little Union Jacks on the domes where identity numbers had featured of late.
These "Ironside" Daleks - the name deriving from the helmet design of Cromwell's New Model Army of the English Civil Wars - were acting in an apparently subservient manner. This was inspired by Power of the Daleks, in which the Daleks found on Vulcan pretend to be servants of human colonists only until they have achieved the independent power supply they need to exterminate everyone.
In the 1966 story, one Dalek chants "I am your servant" over and over, and in his story Gatiss has one state "I am your... soldier", with a pause on the "s" by way of an homage.
Churchill's line about giving the Devil a favourable reference if Hitler invaded Hell came from a real speech the PM made in June 1941. Then, he was referring to support for Stalin against Hitler, despite being a staunch anti-communist.
Gatiss used other Churchill-isms, such as KBO (Keep Buggering On) and "Action this day" which he added to orders which he wanted carried out immediately.
It was Moffat who decided that the Doctor and Churchill should have previous history, inspired by the name-dropping Pertwee's Doctor used to indulge in (Napoleon, Nelson etc).
Labour politician Clement Atlee features at one point attending a meeting in the Cabinet War Rooms. He would go on to win the post-war General Election, which ushered in the National Health Service etc.
You can visit the War Rooms today. Built beneath Whitehall, entry via King Charles Street, they are now named after Churchill.
Professor Bracewell's supposed origins in Paisley, the city SW of Glasgow, is a nod to Moffat. It's his home town.
The Daleks have been creating humanoid robots ever since they copied the Doctor in The Chase.
The story arc continues with another sighting of the crooked smile crack - this time in a wall behind where the TARDIS landed.
Next time: the Angels are back - and so is River Song.