Bottle universe

A bottle universe was a phenomenon in which the entire contents of a universe were scaled down and placed within a bottle. 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)

There was a series of bottle universes within bottle universes; many of which had versions of Time Lords inside them. (PROSE: Dead Romance, Interference - Book Two, Alien Bodies) Several times, Time Lords made attempts to migrate from their bottle universe to the bottle universe inside their bottle universe in order to escape from powerful danger. (PROSE: The Ancestor Cell, Dead Romance, Interference - Book Two)

The universe of the War
While meditating in Qixotl's ziggurat, Kortez journeyed into the astral plane and had a vision of the Doctor wearing a shroud saying that their universe, the universe home to the War in Heaven, was inside a bottle, and that one day, the bottle would break. (PROSE: Alien Bodies)

I.M. Foreman's bottle
I.M. Foreman created the bottle universe and played with the mechanics of it while on Foreman's World. A version of the Seventh Doctor lived inside it. It was stolen from her by the Time Lords while she and the Eighth Doctor slept. (PROSE: Interference)

The Time Lords planned to use I.M. Foreman's bottle universe as a haven from the Enemy. Greyjan the Sane proposed the hypothesis that the Enemy were actually ancestor cells energised by the leaking bottle. (PROSE: The Ancestor Cell)

Seventh Doctor's bottle
In the universe inside Foreman's bottle, (PROSE: Dead Romance, Interference) the Seventh Doctor acquired a bottle universe by the time of his encounter with the Carnival Queen.

Chris Cwej and Marielle Duquesne discovered the bottle universe mounted in the corner of a brass room in the Doctor's TARDIS. They looked inside and saw the version of San Francisco inside the bottle; Cwej observed that the version of the Doctor inside the bottle had parked his TARDIS there. (PROSE: Christmas on a Rational Planet)

Christine Summerfield's home universe
Another bottle universe was created by the sphinxes for the Gods of Dellah and secured by Chris Cwej while he was working for the Homeworld. Cwej opened a gateway for the Time Lords to invade and destroy the bottle universe version of 1970s Earth. (PROSE: Dead Romance)

Marnal's bottle
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)

Others
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)

Merging of bottle universes
"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

After the Time Lords of the War 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, the four-dimensional nature of the Vortex caused a leak in the bottle and its universe began seeping out.

Kristeva heard loa whispering that the complete mixing of realities was inevitable. (PROSE: The Ancestor Cell)

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)

Behind the scenes

 * 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.