The rowdiness of the classroom seems like how it usually is in Modern Magecraft Theories, but there is something wrong with Lord El-Melloi II's behavior. Luvia, who had come to visit and attend one of his lectures, asks Gray the reason why, and it turns out it's because his favorite tearoom has basically closed shop. Lord El-Melloi II heads to the tearoom to inquire on their circumstances as he realizes work just can't progress at this rate, but when he goes down into the sewer system to investigate, an ominous shadow attacks him. Gray, worried that he hasn't shown any signs of returning from the investigation, seeks help from Flat and Svin.

Primary Lecturer Wills is an authority in the Spiritual Evocation division. His father, Sir Trevor, owned the Marburry Workshop that utilizes an entire wasteland to operate as a Magical Workshop. However, the Workshop went out of control, causing many casualties including that of Sir Trevor himself. Lord El-Melloi II, seeking assistance from Spiritual Evocation in order to participate in the Holy Grail War, begrudgingly accepts the request to solve this case. However, what awaited the entourage who arrived at the mansion was Hishiri Adashino, a member of the Policies Department that investigates and enforces rules within the Clock Tower.

One peaceful day, Gray heads by herself to see Reines. With an unexpected turn of events, the two head out to Carnac, an established department store, to go shopping. Not accustomed to shopping in a department store, Gray continually is at Reines' mercy. Furthermore, Luvia coincidentally joins the two midway, causing the three girls to start a tea party.

An incident occurs where Trisha Fellows is murdered by someone aboard the Rail Zeppelin. Lord El-Melloi II undertakes the investigation for the case, but Olga-Marie has doubts about his way of life as it is far from how a Mage should act. Meanwhile, Shishigou and Luvia, under Reines' orders, are conducting their own investigation. The Mystic Eyes Collection Train begins its procession once again, and a mysterious figure appears before Lord El-Melloi II and Gray. The assailant who descends upon the pair with overwhelming power is the materialization of a Heroic Spirit engraved into human history... A Servant.

While giving the gravely wounded Lord El-Melloi II an arduous treatment, Gray and the others harbor doubts about an existence of a Servant whose Master is nowhere to be seen. Shishigou and Luvia are continuing their investigation in London where they visit Jean-Mario Supinerra and inquire about a serial murder that took place seven years ago. The respite was momentary as the course of the Rail Zeppelin has been altered, and the train plunges into the Forest of Dead Apostles, the Child of Einnashe. Gray, worried about the weakened Lord El-Melloi, decides to assist Karabo's group that is acting to resume the train's progress. Furthermore, Melvin, who has arrived at the Mystic Eyes Collection Train after hearing of rumors, joins the entourage. Olga Marie, barricading her lonely self after refusing to help Gray, finds a "certain something" in her own room.

As Adashino's deductions are playing out, Lord El-Melloi II makes his comeback. He sees a clue to the identity of the true perpetrator of Trisha's murder from Gray's testimony, and requests Melvin to delay the Mystic Eyes Auction from starting. His objective is to seek assistance from Olga Marie, and grasp conclusive evidence to overturn Adashino's deductions. Meanwhile, in London, Shishigou gathers up Flat and Svin in order to proceed with certain preparations. As each of them reflect upon their own ideas, the fated Mystic Eyes Auction finally begins.