Metaphysics was a branch of philosophy which included, among other things, causality and the question of the improbability of one's own existence. (PROSE: Separation Day) Andrea Quill thought that metaphysics were not real; only thoughts. (TV: The Metaphysical Engine, or What Quill Did) Emily Rutherford thought it was just an idea, which didn't correspond to anything real. The Third Doctor identified this as a natural mistake, "but it's a serious one".

The metaphysical engine allowed for travel to locations based on thought alone, rather than actual physical space. (TV: The Metaphysical Engine, or What Quill Did) The TARDIS was also a metaphysical engine, capable of travelling into the dimension of a person's mind, their imagination. (PROSE: Every Day)

Mictlan, the extra-dimensional home of the Time Lord faction known as the Celestis, was described to be a "metaphysical bomb shelter" as it was constructed from only ideas and concepts to exist outside of normal space-time. (PROSE: The Taking of Planet 5)

Ashley Lawrence was a metaphysics student at the Braxiatel Collection. (PROSE: Careless Talk) Abney was a student at a special school frozen in time, and an expert in metaphysics. (PROSE: Long Term)

Pilgrim was a Cardiff-based discussion group on metaphysical and philosophical matters such as the meaning of life and the existence of God. (TV: They Keep Killing Suzie)