The TARDIS arrives a space ark, ten million years in the future. The ship is carrying humanity from the doomed Earth to its new home, the planet Refusis Two. Most of the passengers are dormant in miniaturised form; only the essential crew is awake, assisted by the subservient alien Monoids. Dodo suffers from the common cold, and it's soon discovered that neither the future humans nor the Monoids possess an immunity. The Doctor must find a cure before the space ark is ravaged with plague... and, seven hundred years later, confront the terrible consequences as the journey to Refusis Two nears its end.

Although it was writer Paul Erickson who formally received the commission for The Ark on May 27th, 1965, its genesis lay with incoming Doctor Who producer John Wiles. He envisaged a serial set on an enormous spaceship, and discussed this scenario with story editor Donald Tosh, who was sceptical that it could be realised within Doctor Who's limited means. Nonetheless, he discussed it with Erickson, whom he knew from working on Compact; Tosh had been the soap opera's story editor, and Erickson had written (ultimately unused) material. Between them, Tosh and Erickson developed Wiles' idea into a storyline, from which Erickson then began composing the scripts.

After drafting the first two episodes, Erickson met with Tosh and Wiles on September 7th. Concern was expressed that the scripts were overly complicated, and the writer agreed to simplify them. He was also informed that, although the adventure had been devised with the companion team of Steven and Katarina in mind, the Trojan handmaiden was now going to be eliminated from Doctor Who, to be replaced by a sixteenth-century French orphan named Anne. In November, these instructions changed again when the production team abruptly abandoned their plans for Anne to accompany the Doctor, and instead replaced her with the modern-day character of Dodo. On January 20th, 1966, Erickson's agent requested that the BBC credit both Erickson and his wife, Lesley Scott, as writers of The Ark. However, it does not appear that Scott actually contributed to the scripts in any way, and Erickson alone retained the copyright.

As recording began on The Ark, new producer Innes Lloyd started trailing John Wiles

Meanwhile, the Doctor Who production office had been in a state of considerable turmoil in the dying days of 1965. This had culminated in the resignations of both Wiles and Tosh in early January. Tosh was replaced by Gerry Davis, beginning with the final episode of the preceding adventure, The Massacre Of St Bartholomew's Eve. The Ark would be the first serial on which Davis would receive sole credit as story editor. Meanwhile, it was around the time that production began on The Ark that Innes Lloyd started trailing Wiles. Although Wiles would still be credited as producer on The Ark, the transition would effectively be complete by the end of recording.

Directing The Ark was Michael Imison who, like Erickson, was working on his only Doctor Who story. Imison viewed the assignment as a punishment meted out by the Head of Serials, Gerald Savory; Imison and Savory's wife, actress Annette Carell, had come into conflict during the making of Buddenbrooks a year earlier. It appears to have been Imison who came up with the idea of creating a visually interesting race of monsters by having costumed actors use their tongues to manipulate a single “eye” set into their masks. These Monoids replaced the original aliens which had featured in Erickson's scripts. It was soon recognised that The Ark would be an expensive serial to make, meaning that savings would have to be found on the following serial, The Celestial Toymaker.

Production on The Ark began on January 24th at the BBC Television Film Studios in Ealing, London, apparently for the effect of the miniaturised Guardian. A further four days were spent at Ealing between January 31st and February 3rd. The first three days concentrated on the Monoid battle on Refusis Two, while the final day was dedicated to material in the jungle aboard the Ark. Some of the latter scenes involved the use of a variety of exotic animals, notably a twelve-year-old Indian elephant named Monica. Bizarrely, Monica was forced to spent the previous night in her van outside Imison's home, after the van's driver was refused permission to park at Ealing. Model filming for The Ark was also conducted at Ealing, on or around February 4th.

After a period of upheaval both in front of the cameras and behind it, some stability was restored to Doctor Who on February 15th, when William Hartnell's contract was extended through the end of the show's third production block (ultimately, The Smugglers). Three days later, on February 18th, recording for The Ark began at Riverside Studio 1 in Hammersmith, London; as usual, each episode would be recorded on consecutive Fridays.

Having initially used a pronounced Northern accent for Dodo, Jackie Lane was now asked to tone this down

The Ark would be Jackie Lane's first full Doctor Who serial as Dodo, following the character's debut in the concluding installment of The Massacre Of St Bartholomew's Eve. Having used a pronounced Northern accent during her introductory appearance, Lane was now asked to tone this down, due to unhappiness with a regular character not speaking proper “BBC English”. This presented a challenge for Lane, because Erickson's scripts were written with Dodo's original speech pattern in mind; nonetheless, the character's accent would all but disappear over the course of the next few episodes.

On February 24th, Peter Purves' contract was renewed for another twelve episodes, through The Savages. However, Innes Lloyd and Gerry Davis had now decided that they wanted to modernise the regular characters, and so this extension was granted with the understanding that it would bring Purves' time on Doctor Who to an end.

Production of The Ark concluded with The Bomb on March 11th. For this installment, Imison broke with the typical Doctor Who recording pattern, in which each scene was taped in story order. Instead, the schedule was partly organised to keep scenes on certain sets grouped together, and also to avoid having to move the bulky Launcher prop any more than was necessary. This was the first time out-of-order recording had been employed on Doctor Who to such a large extent; it would be a sign of coming changes to the way the programme was made.

• Doctor Who Magazine #228, 2nd August 1995, “Archive: The Ark” by Andrew Pixley, Marvel Comics UK Ltd.
• Doctor Who Magazine Special Edition #7, 12th May 2004, “I'm Into Something Good” by Andrew Pixley, Panini Publishing Ltd.
• Doctor Who: The Complete History #7, 2018, “Story 23: The Ark”, edited by Mark Wright, Hachette Partworks Ltd.
• The Doctor Who Production Diary: The Hartnell Years by David Brunt (2024), Telos Publishing Ltd.
• Doctor Who: The Handbook: The First Doctor by David J Howe, Mark Stammers and Stephen James Walker (1994), Virgin Publishing.
• Doctor Who: The Sixties by David J Howe, Mark Stammers and Stephen James Walker (1992), Virgin Publishing.