Taking place 10 years after the events of Fate/Zero and 2 months before the events of Fate/stay night, the story focuses on Lord El-Melloi II, formerly known as Waver Velvet, a successor of Kayneth and former master in the last Grail War, who is now a professor under the ranks of the Mage's Association. In his years as a professor in the Clock Tower, he is acting as the temporary head of the El-Melloi household until a proper successor can take over. But when strange mysteries involving magic start happening around London, he teams up with a mysterious person and apprentice named Gray in solving many mysteries and cases involving magecraft and hidden conspiracies driving the Mages' Association.