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.

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.

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.

King of Conquerors Iskandar's Relic was stolen from Lord El-Melloi II's possession. An invitation from Rail Zeppelin, the train said to have dealings of Mystic Eyes, was left in its place. Lord El-Melloi II, with Gray and Caules in tow, head towards Rail Zeppelin. Various faces have gathered at the train, such as Hishiri Adashino from Policies, Yvette from the El-Melloi Class, Olga-Marie Arsimilat Animusphere who is the daughter of the Lord of Astromancy, and even Karabo Frampton from the Holy Church. The train departs, together with the various agendas of the passengers...

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.

Gray and the Servant Hephaestion clash within the Child of Einnashe. However, they are engulfed in an avalanche, inevitably forcing a cease-fire. While they temporarily sheathe their weapons, they speak to each other about their ideologies about the relationship between Masters and Servants. Shishigou and Luvia find out that Trisha was investigating about the serial murders from seven years ago and about the Holy Grail War, and see the link between her and the Rail Zeppelin. As various speculations intertwine, Adashino begins to disclose her own deductions in place of Lord El-Melloi II aboard the Mystic Eyes Collection Train...