Journey to the Centre of the TARDIS

Journey to the Centre of the TARDIS borrows from various TV stories, NAs, and EDAs. But, more than anything, it seems like a story written to explore some ideas raised by the NA Cat's Cradle: Time's Crucible and a few other novels—ideas that The Doctor's Wife could have, but didn't (whether because it was written by outsider Neil Gaiman, who never read any of the novels, or because there were already too many ideas to explore).

Damaged TARDISes

With a few minor exceptions (notably season 1's The Edge of Destruction), Time's Crucible is really the first story about the consequences of a damaged TARDIS. In this novel, the Doctor's companion Ace and a group of outsiders are trapped in a damaged TARDIS, caused by collision with another vessel while under emergency operations. They're beset by what ultimately turn out to be future versions of themselves, and the Doctor later explains that this is possible because, inside a damaged TARDIS, time cannot flow normally. Some of the present-day outsiders also cause problems by betraying the others through their own selfishness.

While many later stories, such as the EDA The Ancestor Cell and series 6's The Doctor's Wife, are "damaged TARDIS" stories, Journey basically follows the same sketch as Crucible, and doesn't add much from those later stories.

However, there are major differences.

First, Crucible has an entire secondary plot full of flashbacks to the early days of Gallifrey. The outsiders are the explorers from the first great Time Scaphe experiment, and as such are connected to the turbulent politics of the last days of the Pythia and the rise of Rassilon. While this story is at times compelling, it's also often silly and sometimes tedious, and the explicit parallels to Greek history and legend are hard to take seriously. This is also the story that introduced the Curse of Pythia and the subsequent Looms, and various other controversial plot elements that annoyed so many fans. The Gallifrey story also has very little to do with the main plot; if the characters had been 49th century human time-travel experimenters, or, say, a space salvage crew, it wouldn't have made much difference.

Also, in Crucible, the TARDIS is fleeing an attacking data-eating organism, the Process, when it's captured by the TARDIS collision. The Process turns into a very silly giant leech monster inside the TARDIS, and becomes the main enemy in the novel. The TV episode has no equivalent. The TARDIS attacks when one of the salvage workers betrays everyone out of greed, but really the future selves are the only real enemy. Simplifying the story by removing the Gallifrey subplot and the Process streamlines it tremendously. Crucible was a long, slow novel, and even it barely had room for all of its ideas; there's no way they could have fit into 45 minutes of TV with any of that. 

The inclusion of the Process and the Time Scaphe also means it's never clear how much of what we were seeing was the consequence of a damaged TARDIS, and how much was caused by other factors, which made the central idea of the story weaker.

Meanwhile, the novel's future selves have been living inside the damaged TARDIS for decades. We discover that the sadistic tormentors are the same characters we've met over the first few hundred pages, even the ones we thought of as heroic, beaten down by decades of futility until they've given up and allowed the Process to enslave them. Journey's future selves are just "time zombies", turned bestial by leakage from the Eye of Harmony. The novel's version of the story allows it to explore the idea that anyone can turn evil, and that definitely adds something the episode is lacking. 

On the other hand, zombies are always good for action scenes, and they're certainly better than the action scenes against the giant rolling leech monster.

Finally, in the novel, the TARDIS is turned "sort of inside out", and appears (at least to Ace) as a ruined city made up of repeated subdivisions, where each one is more dilapidated than the previous one. This is a fascinating image, and it vividly illustrates how the TARDIS bends space and time into each other. On the other hand, it also means that we don't actually know that's what we're seeing until most of the way into the book. And it means we don't get the TARDIS runaround that Journey gives us.

Inside the TARDIS

Most of the show's TARDIS scenes, both classic and new, take place in the console room. Two Fourth Doctor stories, The Masque of Mandragora and The Invasion of Time, show much more of the interior, including a collection of wildly incongruous rooms, like the famous municipal indoor swimming pool. However, Logopolis and Castrovalva show a handful of rooms that all match the console room, with white roundeled walls.

The NAs and EDAs largely ignored the Castrovalva look in favor of the eclectic style of Invasion. The novels explained time and again that the TARDIS was "potentially infinite", and contained rooms beyond describing. Sometimes we even saw some of them. Most notably, the EDA Vampire Science introduced an meadow full of butterflies, with no walls or ceiling, which featured in a number of later novels. (Time's Crucible had earlier shown that such a thing was possible, but not necessarily normal, as the TARDIS was described as "sort of inside out" at the time.)

The series 6 episode The Doctor's Wife, and scenes from some of the official video games before it, seemed more in keeping with Castrovalva. But Journey followed Invasion and, especially, the EDAs, by showing off what's possible inside a TARDIS. In particular, it had the first on-screen view of an outdoor area within the TARDIS.

It's pretty clear from both promotional materials and statements by the producers that the chance to do a real TARDIS runaround, better than the one they didn't have time for in Wife, was a large part of the reason for making this episode.

The Eye of Harmony

In its only two mentions in the classic series, The Deadly Assassin and The Invasion of Time, the Eye of Harmony was the power source of Gallifrey. These two stories notoriously contradict each other in many regards, but at least that was a constant, and remained so throughout the NAs. However, in the TV movie, the Eye of Harmony is in the Doctor's TARDIS.

The first EDA, The Eight Doctors, explains away this contradiction by claiming that the Eye of Harmony in the TARDIS is both a symbolic manifestation of the power source on Gallifrey, and a link to that power. The Adventuress of Henrietta Street and The Gallifrey Chronicles (and, to a lesser extent, the PDA The Quantum Archangel) later added to this explanation.

The TV movie also introduced the idea that if the Eye "leaks", it can damage space-time. The Eight Doctors followed up with the idea that a leaking Eye would giving visions of the past, and possibly the future. Neither of these ideas had been mentioned in the new series before becoming plot points in Journey.

Historical Secrets

Journey also shows Clara discovering and reading a book, The History of the Time War, that can't possibly exist. Of course the TARDIS is full of things that can't exist, as the novels told us repeatedly, and The Doctor's Wife at least hinted. But this is a particularly interesting thing.

Larry Miles's spinoff series, Faction Paradox, begins with The Book of The War, a sort of novel in encyclopedia form. This book encodes "forbidden knowledge" out-of-universe as well as in-universe—in particular, the "key" that connects Faction Paradox to elements of the Doctor Who Universe which Miles doesn't have a license to use. In particular, it tells you that Grandfather Halfling in FP is really the Doctor in DW. And the book in Journey tells Clara who the Doctor really is.

This also connects up with Time's Crucible again. It's not entirely clear what the Cartmel Masterplan actually was, but Marc Platt (one of Cartmel's stable of writers toward the end of the TV series, and the author of Crucible) clearly believed that the main idea was that the Doctor was actual a reincarnation of the Other, a mysterious character from early Gallifreyan history whose existence is first hinted at in Crucible (and Platt's novelization of Battlefield at around the same time).

Finally, this loosely connects Clara with Fitz from the EDAs. In a loose arc running from Escape Velocity to Halflife, Fitz gradually remembers/discovers the Doctor's role in destroying Gallifrey, and believes that he's the only person in the universe who knows the truth. In the novels, this never really went anywhere interesting. The Doctor also eventually remembered the truth, and then we met a number of other people who knew it, and eventually it became irrelevant anyway. In the upcoming TV stories, Clara's memories may become much more important.

Summary

Overall, it seems clear that the main motivation for this episode was the chance to do a proper TARDIS runaround, showing us the wide variety of environments that she contains and exploring her inner workings.

Given that constraint, the main story was borrowed from Time's Crucible, but ruthlessly stripped down to remove the extraneous subplots that would have slowed things down. This means a few interesting ideas were lost as well.