The longest-running science fiction TV show in the world, Doctor Who, turns 50 this year – even that milestone dwarfed by the nine centuries old the titular Doctor claims to be. Since the show’s first episode was transmitted by the BBC in November 1963, nearly 800 episodes of the show have been shown. Thanks to DVDs and the occasional repeats season, these old shows have a life the programme’s originators would have thought as fantastical as the time-travelling TARDIS or the monsters that have been permanent fixtures of Doctor Who for five decades. However, more than a hundred of the episodes broadcast in the 1960s may never be seen again. While Daleks, Cybermen and other monsters and villains have attempted to wipe the (fictional) Doctor from existence throughout his half-century of travels through time and space, the beings responsible for erasing some of his earliest adventures have a more prosaic origin: the BBC itself. Though, true to the show’s extra-dimensional spheres of action, it was all a matter of space.

Early archive material was held on vast reels of 16mm tape, sealed in metal canisters for protection. By the 1960s and 70s the BBC archives were already stuffed full from three decades of transmissions. The decision was taken to “downsize” the accumulated recordings to make way for fresher material. A representative sample of each programme – from Dad’s Army to Dixon of Dock Green and Doctor Who – would be retained, while other recordings would be junked, sometimes as soon as two months after broadcast. The view was that nobody would be able to watch these old black-and-white programmes, even if they wanted to, and since affordable home video players then seemed as outré as the moonbases and distant satellites Doctor Who visited, you can almost see the archivists’ point.

So the junkers went in. Little forethought seems to have gone into their choices of what to erase and what to save. In the 60s, Doctor Who stories typically ran to around six 25-minute episodes; in some cases, the junkers would retain a single episode from the middle of a story and destroy the remainder. A few stories lost only one or two episodes, but in many instances, the entirety of a story was wiped. No footage remains, for instance, of the series’ first adventure in history, “Marco Polo”, designed to meet the show’s original remit to educate as well as entertain its young viewers. No episodes remain of “The Macra Terror”, in which giant crabs terrorise an outer-space Butlins holiday camp; nor of the snappily-titled “The Massacre of St Bartholomew’s Eve”, which, were it still to exist, would be quite the argument that kids today have it easy, with their Iggle Piggle and their Tree Fu Tom: in 1966, Britain’s children were being entertained by an adventure about warring religious factions in Catherine de Medici’s France. With illustrative woodcuts.

No episodes remain of “The Macra Terror”, in which giant crabs terrorise an outer-space Butlins holiday camp; nor of the snappily-titled “The Massacre of St Bartholomew’s Eve”

And while one might assume that the presence of the series’ most enduring villain might be reason to preserve a show, out went all six episodes of “Power of the Daleks” – arguably the pivotal Doctor Who story. For, as well as the Daleks, this was also the first story to feature Patrick Troughton, who took over from original Doctor Who William Hartnell in the series’ most outrageous and important “twist”: When Hartnell’s Doctor – an elderly cove, alternately chipper and curmudgeonly – collapses on the floor and transforms into an entirely different man, this was Doctor Who the show making a bid for the same immortality its central character suddenly seemed to have. By establishing that the eponymous Doctor might look or behave any number of ways and yet remain fundamentally the same character no matter what face he wore, Doctor Who shouldered its way into a surprisingly short list of modern myths capable of being reanimated and reinterpreted forever more, enduring as Sherlock Holmes or Robin Hood. (A few years later, the James Bond films would pull the same trick, only without having to invoke bafflegab about “regeneration”, or design special effects to show Sean Connery metamorphosing into George Lazenby in a blaze of energy – rather a shame, really.)

The full episode is listed as one of the ten most sought-after “missing” BBC programmes

Footage of that first metamorphosis, as the craggy features of the first Doctor are bathed in electronic effects before becoming the sallower, jowlier face of the second Doctor, only exists because of another, unwitting, BBC archivist. Bizarrely, only the final episode of this final adventure for the first Doctor, “The Tenth Planet”, was junked as well – all but a few minutes of footage showing that first regeneration, which was copied and broadcast by that other stalwart BBC children’s show, Blue Peter. The full episode is listed as one of the ten most sought-after “missing” BBC programmes, putting it on a par with recordings of another outer-space escapade of a few years later: the channel’s broadcasts of the moon landings in 1969.

Since then, a slow and erratic trickle of “lost” material has found its way back to the archives. Some, like that errant footage from “The Tenth Planet”, turned up as clips in other shows. Private collectors – including some buying job-lots of old film canisters at car boot sales – have done the honourable thing and returned random episodes. And über-fan and pop producer Ian Levine, who worked in an unofficial capacity at the BBC in the late 1970s, recounts afternoons spent clambering into skips to rescue material bound for the rubbish dump – including all seven episodes of “The Daleks”, Doctor Who’s second-ever story, and the first appearance for the metal monsters. (He also recorded a Live Aid­-esque protest song when Doctor Who was briefly on hiatus in 1986, but let’s not dwell on that. Nor Google it.)

A combination of dogged persistence, painstaking research and sheer blind luck has helped bring some long-lost Doctor Who home. Perhaps the oddest discovery was that of two episodes of “The Daleks’ Masterplan”, an extraordinarily ambitious 12-part adventure from 1965 (reputedly commissioned at the insistence of the then BBC Controller, whose mother was a big Dalek fan). In the episodes, some white mice are sent through a “molecular disseminator”, the Doctor is attacked by an invisible monster, and the Daleks invade ancient Egypt in pursuit of the Doctor, exterminating pyramid-building slaves as they go. The recovery of the episodes involved no less bizarre a juxtaposition: they were in an old film canister found in the basement of the Church of Latter-Day Saints in Battersea, London. The discovery sparked a brief but fervent search of church halls and basements around the UK. Sadly, this search didn’t turn up any more missing episodes – nor did it explain what the Mormons had wanted with the film in the first place (though the story does feature a time-travelling monk with mischievous intentions, which might offer a clue).

Farther afield, in Australia, two fans researching in the country’s National Archives in 1996 uncovered film that contained not a full episode or story, but a series of clips excised from Doctor Who stories to make them suitable for broadcast to a seemingly rather timorous population. The resulting compendium of stabbings, zappings, roaring Yeti and Macra monsters lurking in clouds of gas makes for a heady but largely unrepresentative showreel of 60s Who. Tantalisingly, the collection indicates that some now-missing stories were bought and broadcast by Antipodean TV stations – but none of the full episodes from which this footage was literally cut have yet been found.

Viewers had to come to terms with the variable acting, the slightly shonky stunts, and the fact the monsters speak in a Stephen Hawking buzz which makes their threats largely incomprehensible

Diligent and enterprising fans in other countries have done astonishing work tracing which television stations in which nations once screened Doctor Who – by the mid-1970s, while the BBC was junking old episodes, the show had been sold to television stations in around 35 countries – and raiding their archives in the hope of discovering TV gold. There seems something very romantic about what must be a largely unrewarding and very dusty process; when a lone episode of 1965 story “The Crusade”, set during the reign of Richard the Lionheart, was found in 1999 (again in New Zealand), it even made the national news in the UK. There was, however, something faintly disingenuous about a BBC news report that crowed the discovery but avoided mentioning quite whose fault it was the episode had been missing in the first place.

The archive-raiders’ dedication was rewarded, too, in 1992, when the entirety of “The Tomb of the Cybermen”, a four-part story starring Patrick Troughton, was found at Rediffusion TV in Hong Kong. The story, long thought a particular highlight of 60s Doctor Who, is the only complete adventure to survive from the 1967 series; of the 40 episodes made that year, only 13 are now known to exist. However, the return to the UK of these much-longed-for episodes – and their swift release onto home video (I remember rushing out on the day of release to buy a story I was too young ever to have seen) – threw up a new controversy. Even its most ardent fans can’t deny that Doctor Who was, for much of its fifty years, made on a budget undeserving of the description “shoestring”. (Defenders of the show have argued that what it lacked in money it made up for in charm and ambition; critics have simply pointed to its wobbly scenery and moments where hapless extras dressed as giant ants stumble headlong into the camera.) When “Tomb” was seen for the first time, following a quarter of a century’s mythmaking (“The ultimate Doctor Who story! The Cybermen have never been so scary!”), much of its mystique vanished instantly. Viewers had to come to terms with the variable acting, the slightly shonky stunts, and the fact the monsters speak in a Stephen Hawking buzz which makes their threats largely incomprehensible. It took quite some time for fans to come to terms with the reality of “Tomb”, rather than its memory. Sometimes – as we listen to the soundtracks recorded off their TV sets by enterprising fans of the show, who had no way of knowing these would be all that would survive of some stories – it’s better to imagine the epic rather than see it as it really is: television made in a tiny studio in Shepherd’s Bush, against the clock, with no time for re-takes to correct flubbed lines or remount dodgy effects.

106 episodes of Doctor Who are still missing, and while the DVD range has released some stories with new animated episodes, set to those original soundtrack recordings, in lieu of missing instalments, it seems unlikely a full story will ever be remade in this way (for artistic as well as commercial reasons). As time goes on, with the archives of every TV station around the globe investigated, the likelihood of more “lost” material being found dwindles.

Occasionally, though, there’s still a happy discovery. This month sees the release on DVD of Episode Three of 1965 story “Galaxy 4”, which was returned to the archives by a private collector towards the end of 2011. It’s the only episode of the story now known to exist, and no matter the merits or otherwise of its script or its realisation (the story calls for no fewer than three different groups of alien creatures, as well as an exploding planet – there’s that ambition again), there will, for fans, be something magical in being able to see one more lost sliver of Doctor Who history slip into place, five decades since it was last seen.

And yet, maybe it’s part of the appeal for enthusiasts that almost one eighth of the history of a programme whose very title poses a question never satisfactorily resolved should remain a mystery. C

The Radio Times has an ongoing appeal for information leading to the recovery of the 106* missing Doctor Who episodes

*On 11th October 2013 the BBC announced that nine of the 106 missing episodes had been found at a TV station in Nigeria