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A bottle universe was an invention of I.M. Foreman; the entire contents of a universe were scaled down and placed within a bottle. The creator had some degree of control over the universe, but many aspects took place of their own accord. (PROSE: Interference - Book One)
History
I.M. Foreman created the bottle universe and played with the mechanics of it while on Foreman's World. It was stolen from her by the Time Lords while she and the Eighth Doctor slept. (PROSE: Interference - Book One, Interference - Book Two)
Chris Cwej worked for the Time Lords in securing the universe in a bottle and opened a gateway for the Time Lords to invade and destroy the bottle universe version of 1970s Earth. (PROSE: Dead Romance)
The Time Lords planned to use the 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)
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)