Arriving in Alexandria, the party decides to split for safety reasons, since Egypt is technically enemy territory (Atlas). Rin and Ergo go check in at their hotel, while Waver and Gray go meet the Atlas person supposed to pick them up. Despite having eaten some basbousa on the train, Gray gets hungry because the amount she eats has recently increased. In the café, Waver was lecturing Gray about the history of her dish, but Karmaglyph needed to correct him on one factoid he got wrong.
Karmaglyph introduced himself to Gray. From his insecure words and demeanor, she could immediately tell he wasn't like any of the other Lords she met. He doesn't have the same air of imposing dignity as the rest, as he self-deprecatingly admits. Naturally, two Lords meeting in Egypt is no coincidence. Waver was expecting to be greeted by someone from Atlas, but it was Karmaglyph who came to pick them up, and Karmaglyph was also the reason why Reines couldn't explain the pharaoh murder mystery over the phone. Waver had to be in person to hear the details because Karmaglyph's project is highly confidential. He asks Waver to keep it a secret that Atlas and the Clock Tower are forming a joint excavation team.
The trio gets to the Pharos lighthouse, while Waver and Karmaglyph complete each other's archeology lecture about it. There were no tourists or employees there because the Meluastea used both magical and legal means to keep people away. Waver finally gets his chance to about Reines's team's situation, and Karmaglyph answers he didn't do them any harm. If anything, he was more afraid of the harm they could do him. Passing through the lighthouse, they reach the location of Atlas's submarine. The law of Atlas says they can't bring weapons outside, but this submarine counts as only a practical public tool instead of a weapon. Besides, anything with proper equivalents on the outside world's civilization level automatically stops counting as a weapon. Anyways, Alexandria's submerged ruins are as insurmountable of a challenge to Atlas and Meluastea as they are to modern science, which is why the joint excavation team is a thing. Waver and Gray were in no position to say no, so Gray simply messaged Rin and Ergo that they were going to the bottom of the sea and got no response before entering the sub.
The bottom of the sea was clearly visible from inside the submarine, as if they were outdoors in the daytime, due to the Atlas sensors supplementing the images. It mirrors one Iskandar myth where he explored the bottom of the sea by diving in a glass barrel tied by a chain and using a lamp to see the fishes in the dark waters. While Gray mused about the relationship between the Iskandar myths and the reality of his life, the submarine passed through the illusory sea floor and she could see the city-sized ruins on the real sea floor. The submarine entered the giant dome and dropped them off. The air inside the dome still had AoG mana. Arriving outside,
Gray immediately ran to hug Reines. She was slightly envious of how Reines grew a bit taller this past month without seeing her.
Reines and Latio explained the situation. The excavation is still ongoing. Karmaglyph was sent to the surface because among the people guaranteed to know Waver by face, he would be the least capable of removing the Atlas tracer. Giuseppe and Quart approach to see the brother Reines told so much about. Reines calls Giuseppe "Mister Sugdime", but he insists he should be called either first name Giuseppe, or something like amore or bello. In contrast to Giuseppe's goofy flirting, Quart is pretty curt with his introduction. He shares a graffiti art gallery with Karmaglyph. He demonstrates his graffiti art by rubbing his hands on a wall and forming an abstract image of the sunset in Alexandria. He then rubs his hand on the wall again, erasing the image because they can't stain the ruins. Waver quickly recognizes that as one of the Traditional Features of the Six Sources. The Eltnam learn special nerves, the Crudelis learn special bones, and the Ishtario learn special skin. Quart paints by manipulating the color, viscosity, transparency, and durability of his skin. Gray speculates that his five-colored hair has to do with how hair and nails are part of the same system as skin. Giuseppe tries to flirt with Gray too, but Waver intervenes demanding them to explain their location. According to Atlas data, the Library of Alexandria had two buildings. The historically famous building collecting all worldly knowledge, and the submarine building collecting all the secret magecraft knowledge that can't go public. Gray associates that concept with the Spirit Tomb, assuming it to be Atlas's version of it. Waver argued that a pharaoh's riches could afford pyramids, but a city-sized library was too much. However, this is justified by Ptolemy's connection to Atlas. Latio goes show them to their rooms instead of continuing the discussion by the library entrance because Karmaglyph, Giuseppe and Quart aren't supposed to know the details of the pharaoh's murder.
The library is annexed to lecture halls and the rest areas they're currently on. About 20% of the place's functionalities were restored by the team. Waver asks why are he and Latio involved in this whole Library of Alexandria joint excavation team deal when they were supposed to be debating Ergo. Latio revealed that the research notes she had were incomplete. She only inherited the information on when Ergo would wake up and a few formulas that Set would render usable. She doesn't know what exactly the ancient Crudelis alchemist was researching because the Atlas law forbids revealing your personal research results to others. This precept sounds inefficient, but the gist of it is that the alchemists consider researching as an individual and researching as a member of the organization to be completely different things. Every alchemist has both an individual research quota and an organizational research quota. Organizational research results are public and anyone can use them to get their personal research moving. Back to Latio's topic, her plan was to capture Ergo first and then figure out her ancestor's personal research from there. But now that she lost her chance at Ergo, her plan B was to peek at her ancestor's research directly. Her ancestor's contract with Ptolemy demanded all research about Ergo to be copied to the Library of Alexandria. Latio found the lost data on the Tri-Hermes about this Atlas-made Library, called Giuseppe's team to excavate it as their organizational research, and they in turn called Karmaglyph as an expert on archeological excavations. Now we're finally getting to the premise of the pharaoh murder mystery. At the present moment, no one can access the contents of the library because someone stole the security key. They know the key is still within the dome because the lights are still on. Also, two team members (Latio's father and Karmaglyph's assistant) are stuck in the second layer until the key is connected again. The second layer is not that fortified (if the security key was connected anyone allowed in the library could enter the second layer with no restrictions), so the team is working on a method to infiltrate the second layer without needing to find the key, but that won't be concluded until tomorrow. The third layer is the real core of the library, and the fourth layer is an even deeper forbidden realm that even the current Atlas technology would struggle a lot to reach. A mechanical bird perches on Latio's shoulder. The bird is Ptolemy's spare body, which Latio activated in secret after the incident. He explains why Reines referred to this theft as the murder of a pharaoh: the ancient alchemists set Ptolemy's heart as the library's security key, so this theft was actually someone gouging his heart out of his mummy.
Meanwhile, at the hotel side, Ergo was reading the Japanese fairy tale book he got from Mana while Rin was charging her gems. He promised Lana before that he'd come back to see his pirate crew again, and now he promised Mana that he'd return her book. Even if he forgets what he promised, the fact that there are people waiting for him is one treasure he won't forget. Rin comments on how Waver and Gray are taking really long to come back, and Ergo pointed out how her phone screen lit up a few times. Rin didn't think she was getting messages because her phone didn't ring. She read that the "Atlas" representative was Lord Meluastea. Ergo didn't know how significant that was, so Rin had to explain that the Department of Archeology is a Clock Tower faculty that never escaped poverty throughout its whole history, but their sheer authority was enough to keep the Meluastea always at the very top of the Neutral Faction without any cash to back it up. Having another Lord from another faction with Atlas is worrisome, but the Meluastea aren't aggressive, so it won't immediately become a battle between departments. Ergo then notices "strings". Rin carefully opens the door, but when she does, Ergo is bound by his own Phantom Hands, which he can't turn off.
Ergo urged Rin to run away and she triggered a smokescreen. With the time it took for Sion to deprogram that, Rin successfully managed to escape from the window. Ergo is left alone with Sion.
Don't worry about Mana's book because Sion picked it up from the floor but also do worry because she's apperently holding it like this. She gets Ergo to stop struggling when she explains how the Etherlite is interacting directly with his brain. He asked why she was after them and Sion explains her current mission is an internal audit. She determined that Lord El-Melloi II was in contact with an Atlas traitor.