Bottle universe

A bottle universe, or universe-in-a-bottle, was a highly complex artefact wherein which a universe, with its own physical laws, was contained wholly within a "four-dimensional Klein bottle" in a more "real" universe. The universe within the bottle could be referred to as a micro-universe.

Some accounts suggested that the reality of the Seventh Doctor's travels with Chris Cwej and Bernice Summerfield and the universe of the Eighth Doctor's travels with Sam Jones were distinct bottle universes. After the Time Lords of the Eighth Doctor's world placed the bottle containing the Seventh Doctor in the Time Vortex, it began to "leak", causing the two realities to retroactively merge into one continuum.

Nature
Rather than all elements within the bottle remaining too microscopic to see from the outside, the physical bottle acted as an interface, able to "zoom in" to anything happening within the bottle universe in accordance with the user's wishes.

The owner of a bottle universe had some degree of control over its contents, but many aspects took place of their own accord. (PROSE: Interference - Book One)

Bottle universes could be deliberately created by such forces as I.M. Foreman, who had to draw considerable power from the Time Vortex to do so, (PROSE: Interference - Book Two) or by the All-High Gods, who jealously guarded the bottle they'd created. (PROSE: Dead Romance) However, bottle universes could also occur naturally when bubble dimensions left the relative dimension in which they spawned, budding off into distinct realities. (COMIC: The Infinite Corridor) The Tenth Doctor believed that it would be impossible to find someone if they were in a bottle universe as it was born in this way. (COMIC: The Infinite Corridor, Old Girl)

A bottle universe's contents would naturally trend towards reflecting the universe in which it had been created, but with a loss of "resolution" the further down the bottle went. If the reality of Chris Cwej's travels with Christine Summerfield was a bottle universe, as Christine speculated (PROSE: Dead Romance) and I.M. Foreman claimed, (PROSE: Interference - Book One) the Time Lords of the "higher" universe would gain godlike powers within the bottle universe. (PROSE: Dead Romance, Interference - Book One) Christine's bottle was so "low-resolution" that there were no Great Houses or other known extraterrestrial influence on its Earth, and the Great Houses took it over with extreme ease when they entered it. (PROSE: Dead Romance)

War in Heaven bottles
One set of bottles, whose boundaries were a matter of contention, were of high strategic significance within the War in Heaven.

I. M. Foreman's bottle
While on Foreman's World, I.M. Foreman created a "universe-in-a-bottle" by diverting huge amounts of power from the Time Vortex, sucking in Father Kreiner along the way. When the Eighth Doctor visited Foreman's World, he was amazed to see a version of his own seventh incarnation within the reality of the bottle. (PROSE: Interference - Book One) The High Council of the Time Lords acquired the bottle, intending to evacuate their reality into it as a haven from the Enemy in the oncoming War in Heaven. (PROSE: Interference - Book One, Interference - Book Two, Dead Romance) There, they became "almost godlike". (PROSE: Interference - Book One) Within Chris Cwej's reality, Christine learned much about mysterious All-High Gods. She came to suspect that they were actually versions of "Cwej's employers" from one universe up, fleeing some great enemy and having acquired immense powers within the bottle. (PROSE: Dead Romance) However, there were other possibilities as to the All-High Gods' identity. (PROSE: Dead Romance, The Book of the War, Twilight of the Gods)

The Kings of Space's bottle
To Foreman's surprise, the denizens of her bottle universe created a bottle universe of their own, (PROSE: Interference - Book One) specifically the Kings of Space, two of the renegade All-High Gods. His "employers", the Great Houses of his reality, told Cwej that the bottle was then stolen by the Evil Renegade, the Great Houses' propaganda-slanted misrepresentation of (PROSE: Dead Romance) the Seventh Doctor. (PROSE: Original Sin) After the Houses caught up to him, they acquired the bottle universe for themselves, intending to flee into it to escape war with the the All-High Gods (PROSE: Dead Romance) much as the Time Lords fled from the Enemy. (PROSE: Interference - Book One) This sub-bottle did not contain any Great Houses, and its version of Earth, where Christine Summerfield was born, was free of extraterrestrial influences until Cwej's employers' arrival. (PROSE: Dead Romance)

Recursion: the Eighth Doctor in a bottle
However, the situation was more complex than it seemed.

While meditating in Qixotl's ziggurat on the margins of one of the Eighth Doctor's adventures, Kortez journeyed into the astral plane and had a vision of a future Doctor wearing a shroud who said: "We are all of us living inside the bottle". (PROSE: Alien Bodies) Just as the Eighth Doctor had seen the Seventh Doctor within Foreman's bottle, (PROSE: Interference - Book One) the Seventh Doctor who fought the Carnival Queen had, within his TARDIS, a bottle in which he saw his bottle-counterpart in San Francisco, (PROSE: Christmas on a Rational Planet) matching the inception of the Eighth Doctor. (TV: Doctor Who) When Spring-heeled Jack looked into the Eighth Doctor's mind, he saw Time Lords in "a dull grey world" in "a bottle he couldn't wait to break". (COMIC: The Curious Tale of Spring-Heeled Jack)

The bottle breaks
"We are all of us living inside the bottle. And one day, the bottle will break. Then all worlds will be one world. The inside will meet the outside."

- Kortez' astral vision of the Doctor

Kortez's vision stated that "one day, the bottle [would] break". (PROSE: Alien Bodies) Indeed, after the Time Lords of the Eighth Doctor's universe stole Foreman's bottle universe, they kept it for safekeeping in the Time Vortex with plans to possibly colonise it to escape the Enemy. However, they had failed to consider that the bottle was only designed to keep its universe contained within a three-dimensional environment. Within the environment of the Time Vortex, which was four-dimensional, the contents of the bottle universe, (PROSE: The Ancestor Cell) originally created by drawing power from the Vortex, (PROSE: Interference - Book Two) leaked back into it, "like throwing an uncorked wine bottie into an ocean at full swell". (PROSE: The Ancestor Cell)

Kortez's vision stated that once the bottle broke, "all worlds [would] be one world. The inside [would] meet the outside". (PROSE: Alien Bodies) Kristeva heard loa whispering that the complete mixing of realities was inevitable. (PROSE: The Ancestor Cell) Indeed, subsequent accounts showed the universe of Chris Cwej and the All-High Gods as one and the same with that of Compassion and the War in Heaven; in fact, The Book of the War suggested that the Gods were directly connected to the Enemy of the War in Heaven, (PROSE: The Book of the War) and Eliza identifying the Great Houses who'd invaded her home, sub-bottle world with those participating in the War in Heaven. (AUDIO: The Eleven Day Empire)

As it broke, the bottle also leaked "untold amounts of unknown energy" into the primary Vortex. The remains of the Doctor's TARDIS, which had been nearly destroyed earlier on, began to calcify around the leaking bottle, using its energy to revive itself and grow into the Edifice. Additionally, Greyjan the Sane believed that the energies of the bottle allowed ancestor cells to grow into shapes unconstrained by established history, allowing them to become the Enemy. (PROSE: The Ancestor Cell)

Other bottle universes
Marnal created a bottle universe when trying to discover the fate of Gallifrey after it had been destroyed. He later used it to track the Doctor through time and to also learn about what kind of person he was and was to become. (PROSE: The Gallifrey Chronicles)

Iris Wildthyme once drank from an unmarked bottle and swallowed a whole universe. (PROSE: Running with Caesars)

Stalls at the First Auction in Heaven sold bottled star systems as paper weights. (PROSE: Going Once, Going Twice)

Behind the scenes

 * The concept of a "universe-in-a-bottle" is a play on decorative, pushing to its farthest imaginable extreme the idea of fitting a large object into a normal-sized bottle.
 * In 1999, author Lawrence Miles intended to explain discrepancies between the Virgin New Adventures and BBC Eighth Doctor Adventures by establishing that the former series was set in a bottle universe located inside the latter. In his novels Interference and Dead Romance, the Gods menacing Bernice Summerfield in the VNAs were identified with the Time Lords of the EDAs, fleeing into the bottle universe to escape the enemy, and gaining godlike powers in the process. However, other authors were more willing to cross the continuities. In the foreword to the 2004 re-release of Dead Romance, Miles admitted that it was a bad idea and rightfully ignored by other authors; this was reaffirmed in The Book of the War, where one of Miles' characters commented that though it wasn't sure whether the universes were the same, it didn't ultimately matter.
 * The concept of bottle universes was referenced in the online collaborative webnovel Our Strange and Wonderful House, where one of the items within the interdimensional Jenny Everywhere Museum was a bottle universe. Our Strange and Wonderful House contained multiple other references to the Doctor Who universe, and the writer of the Museum segment would later reference This Town Will Never Let Us Go in a later Jenny Everywhere novel.