It's been a little while since I played through The City Beneath, but here's the long detailed version as I remember it (assuming you remember what happened in Journey to Rooted Hold). I'll put it in secret tags in case anyone's reading this who hasn't played The City Beneath yet.
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After months of travelling, Beethro finally reaches Rooted Hold, the city of the Rooted Empire. He's there to find out why the Empire is tunnelling into other people's dungeons, and to find Halph, who ran away from Beethro at the end of JtRH. (Beethro's only lead is that he was offered a job as an Architect some months ago.)
Upon reaching the City, he first finds the Infohut, whose occupant tells him that the seat of authority of Rooted Hold is located at Lowest Point, at the bottom of a three-mile deep abyss. Beethro elects to take the long way down, through the Three Gates of the city.
The first gate, the Gate of Sheathing, is passed by Beethro sheathing his sword. The second gate, the Gate of Namedness, requires Beethro to have an occupation in Rooted Hold, and therefore a name (recall that all the characters who reside below ground are named after their jobs, e.g. 39th Slayer). Beethro visits the Naming Office but is told that abovegrounders aren't allowed jobs in Rooted Hold. Beethro explores what little of the city he can access and encounters a familiar face, 84th Negotiator, who had previously tried to warn him away from investigating the Rooted Empire. On this occasion, the Negotiator agrees to help Beethro, if only because she finds the Rooted Empire's bureaucracy stifling and hopes that Beethro might shake things up a little. For the time being, she directs him to the Grand Library.
At the Library, Beethro unsuccessfully tries to research the "Mothingness," a term which the Pit Thing from JtRH used frequently without ever defining it. Beethro explores the Unctuarage instead, in which he encounters the Pit Thing for the first time in months. The Pit Thing directs him to a section of the Library that is in disrepair, allowing Beethro to explore below the library. Here, the Pit Thing redirects Beethro to his hometown of Dugandy for answers. Beethro returns to the city, finds an express route to Dugandy and heads back to the surface of the Eighth.
In Dugandy, he discovers that his own guild, the Smitemaster's Guild, has been working with the Dungeon Architects' Association to cover up the existence of Rooted Hold. He also finds that his restaurant has been demolished. Beethro infiltrates the castle to confront King Dugan directly, but the king is unsympathetic, and Beethro is forced to retreat back below the surface. On his way back to Rooted Hold, he finds a chamber full of holding vats being visited by "1A", the 1st Archivist. The Archivists are in charge of the collection and documentation of knowledge. 1A seems unfazed by Beethro's search for answers, but warns him that the vats contain Aumtlich, which seem to be killing machines better than the Slayers.
Beethro reaches Rooted Hold and meets the Negotiator, who has been busy - thanks to her, abovegrounders can now be named. Beethro returns to the Naming Office and applies to be a Slayer. He passes the test, becomes 256th Slayer (that number may be wrong, but you get the idea) and passes through the Gate of Namedness.
The third gate, the Gate of Firsts, requires that Beethro be promoted to the 1st of his occupation. Beethro can now access a number of more important structures in the city. He finds the Dungeon Architects' Association headquarters, in which he finally finds Halph, studying to be an Architect. Halph doesn't want to join Beethro again, though. Beethro also finds the Patronage, whose occupants seem to oppose the Archivists' plans, and the Slaymaster's Hall, in which the Slayers are due to have a meeting.
Beethro heads to the Archivists' headquarters to gain a pass to this meeting, but 1A orders the Archivists not to give him one. Beethro obtains one anyway by chasing down a hapless clerk, and attends the meeting. There, 1A announces to the Slayers the Archivists' plans for the upcoming Grand Event. Above the surface, 1A explains, knowledge is produced at an incredibly rapid rate - whereas Rooted Hold is politically stable, the countries above ground constantly create and dispose of kings, wage war, etc. Thus, the Archivists reason, if they send a load of troops (Slayers, etc) to the surface to wipe out all abovegrounders, the production of knowledge will be stemmed and the Archivists can actually do their jobs.
Beethro is naturally horrified at this reasoning, and flees the Slaymaster's Hall, stopping only to destroy it (by using bombs to blow up the hall's structural supports) to kill the rest of the Slayers and hopefully delay the Grand Event. His escape takes him to the Rooted Hub, a network of tunnels connecting Rooted Hold to every major settlement on the Eighth. Beethro takes the tunnel to Estengard to try to warn someone about Rooted Hold. Its ruler promises to hear Beethro out if he helps him with the pirates plaguing the nearby waters. Beethro kills the pirates, returns to Estengard to talk with the ruler, and that's where you are now.
Whew. That's actually a lot more plot than I thought there was in DROD. I think that's everything.
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formerly MHighbrow