As one of the Lords of the Clock Tower as well as the department head of the Modern Magecraft Theories department, Lord El-Melloi II holds yet another lecture for his diverse array of students. After the post-lecture meeting with other Clock Tower nobility, he throws out a few insults at the fellow Lords that are interested only in their internal power struggle, but he quickly receives a counter-curse in retaliation. On the following day, while in transit with his apprentice Gray, he notices a cat ran over by a car. It's the stray cat that frequently visited his room as of late. Lord El-Melloi II realizes that this was an attempt to take his own life, and commences a perpetrator hunt along with Gray, Flat and Svin.

Waver Velvet, who fought side by side with Iskandar during the Fourth Holy Grail War, receives a visit from Reines El-Melloi Archisorte and Melvin Weins. Reines asks Waver to help her with something as payment for the debt.

The difficult issue Reines and Melvin brought up with Lord El-Melloi II was a case involving a former student of his, Mary Lil Fargo. Mary is the only daughter of the Fargo family, a branch of the Animusphere family that rules over the Astromancy division. Responding to Mary who felt she needed her former mentor's assistance, Lord El-Melloi II and Gray visit the Fargo estate to witness the dismantled corpse of Mary's father, Ernest Fargo. Disjoined from traditions of Astromancy, the crime scene is representative of Modern Magecraft. Lord El-Melloi II dives in to elucidate the matter.

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.

As the investigation in Marburry Workshop continues, lightning strikes yet again to create a new victim. Lord El-Melloi II and Hishiri Adashino once again are on opposing grounds concerning the perpetrator of this case. Lord El-Melloi II seeks the help of the Necromancer Kairi Shishigou to reinvestigate. Gray and Shishigou are assaulted by a fierce beast, the Black Dog, that suddenly appeared before them. Based on the fact that the Black Dog reacted to Gray's Mystic Code, Lord El-Melloi II elicits a certain conclusion. He then starts preparing for a ritual with the assistance of all Mages who were gathered at Marburry Workshop.

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.

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.

Caules Forvedge is suddenly apprehended as the perpetrator. As Lord El-Melloi II causes the Mystic Eyes Auction to pause while disclosing his deductions, Reines, who is supposedly still in London, rushes over to his side. Thus, Lord El-Melloi II points out the name of the true perpetrator.