The Auditors convince a young clock maker, Jeremy Clockson, in Ankh-Morpork to build a perfect glass clock. They do not reveal that this will imprison Time (the anthropomorphic personification) and thereby freeze time (the physical quantity) on the Discworld. By freezing time, the Auditors intend to eliminate the unpredictability that humans cause through their everyday actions. Death discovers their plans, but is unable to act directly because of the Rules of the universe. Death sends his granddaughter Susan to stop them.
Meanwhile, in a distant valley, a young apprentice of the History Monks, Lobsang Ludd, and his old teacher, Lu-Tze, called 'The Sweeper', hear that a glass clock is being built. Lu-Tze knows of such a clock's side-effects, since he was sent, but failed, to prevent a previous clock from being built. He and Lobsang head for Ankh-Morpork to stop Jeremy from building it.
The Auditors were using one of their own as an agent when contacting Jeremy. Myria LeJean took a human form and became quite disturbed by "her" experiences as "she" became more human and individual, as opposed to the collective Auditors. As she begins to understand more about humans, she opposes the activation of the clock and she eventually joins with Lobsang and Susan to defeat the other Auditors who have also made themselves human. After the resolution, she ends her own life by diving into a vat of high quality chocolate.
- Thief of Time features the neologism 'substition' (first used by Pratchett in Jingo), a term denoting the opposite of superstition.
'No, they're a 'substition', said Susan. 'I mean they're real, but hardly anyone really believes in them. Mostly everyone believes in things that aren't real.'
- A number of the oddities noted by Susan as evidence that the timeline was fractured had previously been commented on by fans. These include the variable dating of Koom Valley; the fact that an Elizabethan theatre was "a new type of building" in Wyrd Sisters, but there was a venerable Victorian Opera House by Maskerade and the uncertainty as to the setting of Small Gods.