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Edit: I simplified the entry I made earlier and added descriptions. This shows a story map of the major plot lines that can be found after "The Desperate Collector." Each map only lists nodes where more than one choice can be made.

* Will destroys Aubrey Blackwell, and takes his library and learning for himself.
The Desperate Collector --> A Slippery Sale --> The House on the Edge of Oblivion --> The Missing Magician --> The New Magician.

* Will apprentices himself to Aubrey Blackwell, but rebels after meeting Frank and Joe Durras.
The Desperate Collector --> A Slippery Sale --> The Magician's House --> Change of Address --> The Vessel --> A Double Cross --> Dealing with the Durrases --> Larceny and Other Larks --> Of Horoscopes --> A Fearful Fate for Two Siblings --> The New Brother --> The Perils of a Paranormal Polygot -->
--> In Which the Author Reveals Their Insecurities: Will's insecurities lead him to rebel against the Stellae.
--> Pieces of the Puzzle That Is Will Prescott: Will's trains with the Stellae.

* Will apprentices himself to Aubrey Blackwell, and winds up replacing his mentor.
The Desperate Collector --> A Slippery Sale --> The Magician's House --> A Yumi Choice --> The Defenestration of Cindy Vredenburg --> A Prisoner in the Attic --> The Space Behind the Face -->
--> Blackwell's Panic: Will teams up with school friends to give themselves new lives.
--> New Information: Will is armed with masks when he meets Frank and Joe Durras

* Will apprentices himself to Aubrey Blackwell, and gets himself a new identity.
The Desperate Collector --> A Slippery Sale --> The Magician's House --> A Yumi Choice --> Of Curses and Worse Things

* Will fights to keep the Libra Personae out of the hands of Aubrey Blackwell.
The Desperate Collector --> Tell Umeko everything --> Umeko wants nothing to do with the book --> Tell him to get lost