What if the Tome of Clear Thought you receive is the real parasite?
The parasite is a viral idea that seeks to spread from mind to mind.
The Tome will not be usable in the conventional way, but its item description will feature a well-meaning message, something along the lines of "Divided we stumble, but together we grow strong. Let us reject our empty urban lives to live in collective harmony." (but better written, pragmatic and convincing)
The item description will continue by encouraging the player to spread the message.
As the player continues their travels, they can occasionally try to convince other NPCs to read the Tome. For example, you could try to convince other Athkatlan Grounds characters, and base game NPCs like Hes, Yarin, Lord Ophal, Harrold and Mrs. Harrold, Radeel, Belmin Gargas, etc...
Some NPCs might be more receptive than others (maybe Ribald turns you down no matter what), and it might be possible for the player to fail if they pick the wrong dialogue options.
And certain wise NPCs (perhaps Temples) might warn the player that not all is as seems with the Tome.
After a number of NPCs have been convinced to read the Tome, some event will occur which tells the player to travel to Southern Edge (or somewhere else).
Gathered there will be all the NPCs who read the Tome. They have been convinced to start a new life embracing the ideas of the Tome.
At this moment, the parasite appears in it's true form. It has planned to feast on those gathered. It thanks you for doing its bidding and offers you power if you are willing to sacrifice those gathered.
The PC can choose to do the parasite's bidding and gain this power, or reject it and fight it in a climatic battle.
(The tricky bit will be in picking NPCs that are important enough for the player to care about them, but not important enough that they can't die without messing up the main game and other mods.)
EDIT: On rereading this, perhaps this will be too predictable to the player! An alternate twist, that some players might not be expecting, is there is no "Evil Parasite" behind this who wants to eat NPCs. Perhaps the virus is just a nonconscious idea - a "memetic" if you will. Maybe the plot can be set up so that the player is expecting an evil outcome, but then the gathered NPCs who read the tome are actually happy, and start living a productive life in Southern Edge (or somewhere else)!
EDIT: Or the author of the Tome could be revealed to be a surprise character with benevolent intentions (perhaps Mairo Mudclapper himself).
