In May 1966, the way Doctor Who stories were presented to TV viewers changed fundamentally. Before then, each episode had it's own title and nearly all linked seamlessly with their immediate successors. From The Savages on, the episodes lost their individual identities and became parts of self-contained stories. However, the practice of linking stories into longer narratives continued until December 1968 and was revived on numerous occasions until as recently as March 1984.

As far as the average viewer was concerned, the first 118 episodes retained their separate identities until the appearance of Malcolm Hulke and Terrance Dicks' ground-breaking book "The Making of Doctor Who" in 1972. This grouped them into 25 stories based on production codes (a series of letters and, later, numbers applied to each group of episodes for the benefit of the actors and production staff), which brought the early stories in line with the later ones, but ignored the fact that many of them formed part of greater wholes. It also ignored the fact that An Unearthly Child was a totally different story to the rest of Story A (known collectively and variously as An Unearthly Child, The Tribe of Gum and 100,000 B.C.), whilst recognising Mission to the Unknown as a separate story to Galaxy Four despite having the same production team and code. It also lumped all twelve episodes of Story V (The Dalek Masterplan) together as one story despite the fact one (The Feast of Steven) had little in common with the other eleven, and two different writers worked on the scripts independently.

Technically speaking, rather than forming 25 or 26 separate stories (depending on your viewpoint), the 118 individually-titled episodes (plus The Savages) can be divided into just seven stories if breaks in narrative are regarded as concluding each story rather than a different production code (which no viewer knew about anyway).

In the mid-1990s, Virgin Publishing introduced a series of original novels supposedly set inbetween the original TV stories. This series is still being produced by BBC Books, and as it grows longer the number of available "gaps" grows smaller, and in some cases non-existent gaps have been filled (by the radio serial The Paradise of Death for instance). These are stories that are definitely or possibly linked.