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A soul was a non-corporeal aspect of a person's essence. It was generally thought to leave the body at the time of death.
According to the Eleventh Doctor, souls were made of stories, not atoms. (TV: The Rings of Akhaten) The soul was sometimes synonymous with a person's mind, their soul being composed of their memories, but even this was not considered accurate. However, the removal of a person's mind to another plane could simulate death, leading to the allusion between a soul and a mind. (PROSE: Timewyrm: Revelation, Falls the Shadow)
Due to being "half-dead" in some metaphysical sense, Origin Zero had the ability to see souls. This allowed her to confirm that the Morch'aliach did indeed trap the souls of the dead within itself, rather then creating mere simulacra. The many souls it had trapped were stuck telling the stories of their own deaths on a loop, which sustained Morch'aliach's existence and helped it deter others from attacking it. The souls were released after P.R.O.B.E. and Ganeida destroyed Morch'aliach. (PROSE: A Honeycomb of Souls)
The souls of the dead passed through the Moon's influence on their way to Heaven, where they were sometimes caught by the Lunaries and offered new bodies. Leonardo da Vinci and Roger Bacon were two such persons who accepted, and by 1590 were still living there. (PROSE: Minions of the Moon)
In the 22nd century, some artists used soul extractors to improve their art, literally extracting portions of their souls and inserting them into the canvas. They used it sparingly, as the results of over-use were lethal. One time when an artist became addicted, he created a living being within the canvas. (PROSE: Untitled)
The neutron eaters tricked Oliver Harrington into bringing more of them through from their dimension by making him think that angels were souls, returning from Heaven to the mortal world. (AUDIO: Lost Souls)
Souls in culture
The Soulless were a group that arose during the Miracle Day event, which had rendered virtually all humans on Earth incapable of dying. Members of the Soulless believed that because they could not die, they had been robbed of their souls. (TV: Dead of Night)
The Time Lords had a rite called Soul Catching, in which a dying Time Lord would transfer his soul to another Time Lord, which would then get assimilated into the Matrix. (PROSE: The Devil Goblins from Neptune)
The early Time Lords under Rassilon`s leadership removed the irrational parts of their souls to create a more rational universe. These removed parts then formed into a gestalt of superstition that eventually became the entity known as the Carnival Queen, the living personification of the Time Lords` irrationality. (PROSE: Christmas on a Rational Planet)
The Cabinet of Souls contained the souls of the Rhodian people after their deaths. Each soul, compressed into a speck of light, could also be used to kill an individual (TV: For Tonight We Might Die) by burning their soul out of existence, burning themselves out in the process. According to Charlie Smith, in the hands of a hero, the souls would take over bodies instead of just burning them. (TV: Co-Owner of a Lonely Heart) The souls were eventually used to destroy the Shadow Kin. (TV: The Lost)
When he revealed that the Krillitanes needed children rather than adults to unlock the Skasis Paradigm because of their imagination, the Tenth Doctor said that they were using their souls as well as their minds to crack the code. (TV: School Reunion)
When the Twelfth Doctor linked his mind with Rusty's, Rusty claimed to see into the Doctor's soul and saw "beauty", "divinity" and the Doctor's "hatred of the Daleks" and saw that "it [was] good". (TV: Into the Dalek)
When aboard the Borg cube that fought in the Battle of Wolf 359, the Eleventh Doctor, when discussing the Borg Collective's theft of free will, began to speak of the true nature of the soul to Amy and Rory Williams only to quickly become distracted. (COMIC: Assimilation²)